From a37678aa176e2cd32077a85ed6642696b39ef6d0 Mon Sep 17 00:00:00 2001 From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de> Date: Thu, 20 Jun 2019 15:39:44 +0200 Subject: [PATCH] Add all MED files --- data/0.0.0/images/AChE-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ANPRA-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ANPRB-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/AP2-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ASCb-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/AcTub-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/AllCR1-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/AllCR2-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Arx-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Ash-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/BAIAP-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/BarH1-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Beta3-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Bmpr1-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Brn3a-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/COE-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Cal2-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Calmodulin-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ChAT-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Chx10-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Dach-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/DbhLike-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/DopaRD2-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR1-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR10-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR12-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR13-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR16-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR19-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR2-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR20-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR22-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR25-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR29-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR3-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR30-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR31-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR32-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR34-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR39-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR4-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR46-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR54-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/ENR57-MED.xml | 39 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+++++++++++++++++++++++++ data/0.0.0/images/GPCR203-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/GPCR209-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/GPCR210-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/GPCR32-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/GPPCR21-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Gata123-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Glt1-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/GlyT-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/GnRH-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/GnrhR-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Grm7-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Gucy-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/HCN1-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/HNF6-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Hand-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Hb9-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Hox5-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Hox7-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Hr38-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Isl-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Kv33b-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Kv33e-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Lhx15-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Lhx2-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Lhx3-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Lmo4-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Lmx1-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Loc28250-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Loc5285ct-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Loc77859-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Loc8913nt-MED.xml | 39 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39 +++++++++++++++++++++++++ data/0.0.0/images/Netrin-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/NeuroD-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Ngb-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Olig-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/P56-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/PCDH15-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/PDF-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/PLCg-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Pax258-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Pax6-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Pde9-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Pea3-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Phc2-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Phox2b-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Pikachu-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/PitxB-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Prdm8-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Prox-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Ptf1-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Pty2-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/RIMS-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Rab3-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Robo-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Scn8aa-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Sema2-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Sim1-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Slit-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Sox2-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Sox4-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/SoxB12-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/SoxB2-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Sp8-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Syt-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Syt12-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Syt7-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Syta-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/TH-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/TIMP-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/TRPV4-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/TRPV5-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Tal-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Tbh-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Tbx20-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/TrpH-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/TrpV-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/Twist-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/UNCS-MED.xml | 39 +++++++++++++++++++++++++ data/0.0.0/images/VAChT-MED.xml | 39 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scripts/files/__init__.py | 1 + scripts/files/copy_helper.py | 14 +++++++++ 204 files changed, 7862 insertions(+), 2 deletions(-) create mode 100644 data/0.0.0/images/AChE-MED.xml create mode 100644 data/0.0.0/images/ANPRA-MED.xml create mode 100644 data/0.0.0/images/ANPRB-MED.xml create mode 100644 data/0.0.0/images/AP2-MED.xml create mode 100644 data/0.0.0/images/ASCb-MED.xml create mode 100644 data/0.0.0/images/AcTub-MED.xml create mode 100644 data/0.0.0/images/AllCR1-MED.xml create mode 100644 data/0.0.0/images/AllCR2-MED.xml create mode 100644 data/0.0.0/images/Arx-MED.xml create mode 100644 data/0.0.0/images/Ash-MED.xml create mode 100644 data/0.0.0/images/BAIAP-MED.xml create mode 100644 data/0.0.0/images/BarH1-MED.xml create mode 100644 data/0.0.0/images/Beta3-MED.xml create mode 100644 data/0.0.0/images/Bmpr1-MED.xml create mode 100644 data/0.0.0/images/Brn3a-MED.xml create mode 100644 data/0.0.0/images/COE-MED.xml create mode 100644 data/0.0.0/images/Cal2-MED.xml create mode 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data/0.0.0/images/PLCg-MED.xml create mode 100644 data/0.0.0/images/Pax258-MED.xml create mode 100644 data/0.0.0/images/Pax6-MED.xml create mode 100644 data/0.0.0/images/Pde9-MED.xml create mode 100644 data/0.0.0/images/Pea3-MED.xml create mode 100644 data/0.0.0/images/Phc2-MED.xml create mode 100644 data/0.0.0/images/Phox2b-MED.xml create mode 100644 data/0.0.0/images/Pikachu-MED.xml create mode 100644 data/0.0.0/images/PitxB-MED.xml create mode 100644 data/0.0.0/images/Prdm8-MED.xml create mode 100644 data/0.0.0/images/Prox-MED.xml create mode 100644 data/0.0.0/images/Ptf1-MED.xml create mode 100644 data/0.0.0/images/Pty2-MED.xml create mode 100644 data/0.0.0/images/RIMS-MED.xml create mode 100644 data/0.0.0/images/Rab3-MED.xml create mode 100644 data/0.0.0/images/Robo-MED.xml create mode 100644 data/0.0.0/images/Scn8aa-MED.xml create mode 100644 data/0.0.0/images/Sema2-MED.xml create mode 100644 data/0.0.0/images/Sim1-MED.xml create mode 100644 data/0.0.0/images/Slit-MED.xml create mode 100644 data/0.0.0/images/Sox2-MED.xml create mode 100644 data/0.0.0/images/Sox4-MED.xml create mode 100644 data/0.0.0/images/SoxB12-MED.xml create mode 100644 data/0.0.0/images/SoxB2-MED.xml create mode 100644 data/0.0.0/images/Sp8-MED.xml create mode 100644 data/0.0.0/images/Syt-MED.xml create mode 100644 data/0.0.0/images/Syt12-MED.xml create mode 100644 data/0.0.0/images/Syt7-MED.xml create mode 100644 data/0.0.0/images/Syta-MED.xml create mode 100644 data/0.0.0/images/TH-MED.xml create mode 100644 data/0.0.0/images/TIMP-MED.xml create mode 100644 data/0.0.0/images/TRPV4-MED.xml create mode 100644 data/0.0.0/images/TRPV5-MED.xml create mode 100644 data/0.0.0/images/Tal-MED.xml create mode 100644 data/0.0.0/images/Tbh-MED.xml create mode 100644 data/0.0.0/images/Tbx20-MED.xml create mode 100644 data/0.0.0/images/TrpH-MED.xml create mode 100644 data/0.0.0/images/TrpV-MED.xml create mode 100644 data/0.0.0/images/Twist-MED.xml create mode 100644 data/0.0.0/images/UNCS-MED.xml create mode 100644 data/0.0.0/images/VAChT-MED.xml create mode 100644 data/0.0.0/images/VAT1L-MED.xml create mode 100644 data/0.0.0/images/VGluT-MED.xml create mode 100644 data/0.0.0/images/VegfR-MED.xml create mode 100644 data/0.0.0/images/Wnt16-MED.xml create mode 100644 data/0.0.0/images/Wnt5-MED.xml create mode 100644 data/0.0.0/images/ascI-MED.xml create mode 100644 data/0.0.0/images/ascII-MED.xml create mode 100644 data/0.0.0/images/asicalpha-MED.xml create mode 100644 data/0.0.0/images/bsx-MED.xml create mode 100644 data/0.0.0/images/catL-MED.xml create mode 100644 data/0.0.0/images/cnga-MED.xml create mode 100644 data/0.0.0/images/dbx1-MED.xml create mode 100644 data/0.0.0/images/delta-MED.xml create mode 100644 data/0.0.0/images/dlx-MED.xml create mode 100644 data/0.0.0/images/edu3to4at6dpf-MED.xml create mode 100644 data/0.0.0/images/edu4to5at6dpf-MED.xml create mode 100644 data/0.0.0/images/edu5to6at6dpf-MED.xml create mode 100644 data/0.0.0/images/eve-MED.xml create mode 100644 data/0.0.0/images/eya-MED.xml create mode 100644 data/0.0.0/images/fezf-MED.xml create mode 100644 data/0.0.0/images/gpb-MED.xml create mode 100644 data/0.0.0/images/gsx-MED.xml create mode 100644 data/0.0.0/images/hox1-MED.xml create mode 100644 data/0.0.0/images/irx-MED.xml create mode 100644 data/0.0.0/images/irx2546-MED.xml create mode 100644 data/0.0.0/images/lbx1b-MED.xml create mode 100644 data/0.0.0/images/lhx6-MED.xml create mode 100644 data/0.0.0/images/mecom-MED.xml create mode 100644 data/0.0.0/images/msx-MED.xml create mode 100644 data/0.0.0/images/muncB-MED.xml create mode 100644 data/0.0.0/images/nAchR-MED.xml create mode 100644 data/0.0.0/images/neog-MED.xml create mode 100644 data/0.0.0/images/ngn-MED.xml create mode 100644 data/0.0.0/images/nk21-MED.xml create mode 100644 data/0.0.0/images/nk22-MED.xml create mode 100644 data/0.0.0/images/nk6-MED.xml create mode 100644 data/0.0.0/images/ntrps-MED.xml create mode 100644 data/0.0.0/images/otp-MED.xml create mode 100644 data/0.0.0/images/paraxis-MED.xml create mode 100644 data/0.0.0/images/rx-MED.xml create mode 100644 data/0.0.0/images/sert-MED.xml create mode 100644 data/0.0.0/images/six12-MED.xml create mode 100644 data/0.0.0/images/six4-MED.xml create mode 100644 data/0.0.0/images/tlx-MED.xml create mode 100644 data/0.0.0/images/trk-MED.xml create mode 100644 data/0.0.0/images/uncx-MED.xml diff --git a/data/0.0.0/images/AChE-MED.xml b/data/0.0.0/images/AChE-MED.xml new file mode 100644 index 0000000..131b370 --- /dev/null +++ b/data/0.0.0/images/AChE-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/AChE-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ANPRA-MED.xml b/data/0.0.0/images/ANPRA-MED.xml new file mode 100644 index 0000000..621e068 --- /dev/null +++ b/data/0.0.0/images/ANPRA-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ANPRA-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ANPRB-MED.xml b/data/0.0.0/images/ANPRB-MED.xml new file mode 100644 index 0000000..2ba6b43 --- /dev/null +++ b/data/0.0.0/images/ANPRB-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ANPRB-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/AP2-MED.xml b/data/0.0.0/images/AP2-MED.xml new file mode 100644 index 0000000..58d5bf2 --- /dev/null +++ b/data/0.0.0/images/AP2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/AP2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ASCb-MED.xml b/data/0.0.0/images/ASCb-MED.xml new file mode 100644 index 0000000..8fd3581 --- /dev/null +++ b/data/0.0.0/images/ASCb-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ASCb-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/AcTub-MED.xml b/data/0.0.0/images/AcTub-MED.xml new file mode 100644 index 0000000..4984413 --- /dev/null +++ b/data/0.0.0/images/AcTub-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/AcTub-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/AllCR1-MED.xml b/data/0.0.0/images/AllCR1-MED.xml new file mode 100644 index 0000000..695d5ed --- /dev/null +++ b/data/0.0.0/images/AllCR1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/AllCR1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/AllCR2-MED.xml b/data/0.0.0/images/AllCR2-MED.xml new file mode 100644 index 0000000..ede90c6 --- /dev/null +++ b/data/0.0.0/images/AllCR2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/AllCR2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Arx-MED.xml b/data/0.0.0/images/Arx-MED.xml new file mode 100644 index 0000000..a7a2756 --- /dev/null +++ b/data/0.0.0/images/Arx-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Arx-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Ash-MED.xml b/data/0.0.0/images/Ash-MED.xml new file mode 100644 index 0000000..f10d0d9 --- /dev/null +++ b/data/0.0.0/images/Ash-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Ash-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/BAIAP-MED.xml b/data/0.0.0/images/BAIAP-MED.xml new file mode 100644 index 0000000..15b25b3 --- /dev/null +++ b/data/0.0.0/images/BAIAP-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/BAIAP-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/BarH1-MED.xml b/data/0.0.0/images/BarH1-MED.xml new file mode 100644 index 0000000..3c0f267 --- /dev/null +++ b/data/0.0.0/images/BarH1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/BarH1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Beta3-MED.xml b/data/0.0.0/images/Beta3-MED.xml new file mode 100644 index 0000000..d0092e6 --- /dev/null +++ b/data/0.0.0/images/Beta3-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Beta3-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Bmpr1-MED.xml b/data/0.0.0/images/Bmpr1-MED.xml new file mode 100644 index 0000000..4f792e1 --- /dev/null +++ b/data/0.0.0/images/Bmpr1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Bmpr1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Brn3a-MED.xml b/data/0.0.0/images/Brn3a-MED.xml new file mode 100644 index 0000000..93d8ae1 --- /dev/null +++ b/data/0.0.0/images/Brn3a-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Brn3a-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/COE-MED.xml b/data/0.0.0/images/COE-MED.xml new file mode 100644 index 0000000..5975be0 --- /dev/null +++ b/data/0.0.0/images/COE-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/COE-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Cal2-MED.xml b/data/0.0.0/images/Cal2-MED.xml new file mode 100644 index 0000000..8aabe6b --- /dev/null +++ b/data/0.0.0/images/Cal2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Cal2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Calmodulin-MED.xml b/data/0.0.0/images/Calmodulin-MED.xml new file mode 100644 index 0000000..af63a1e --- /dev/null +++ b/data/0.0.0/images/Calmodulin-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Calmodulin-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ChAT-MED.xml b/data/0.0.0/images/ChAT-MED.xml new file mode 100644 index 0000000..f8fcfd3 --- /dev/null +++ b/data/0.0.0/images/ChAT-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ChAT-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Chx10-MED.xml b/data/0.0.0/images/Chx10-MED.xml new file mode 100644 index 0000000..6d12d7a --- /dev/null +++ b/data/0.0.0/images/Chx10-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Chx10-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Dach-MED.xml b/data/0.0.0/images/Dach-MED.xml new file mode 100644 index 0000000..0a9e15d --- /dev/null +++ b/data/0.0.0/images/Dach-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Dach-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/DbhLike-MED.xml b/data/0.0.0/images/DbhLike-MED.xml new file mode 100644 index 0000000..b530976 --- /dev/null +++ b/data/0.0.0/images/DbhLike-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/DbhLike-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/DopaRD2-MED.xml b/data/0.0.0/images/DopaRD2-MED.xml new file mode 100644 index 0000000..0af286d --- /dev/null +++ b/data/0.0.0/images/DopaRD2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/DopaRD2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR1-MED.xml b/data/0.0.0/images/ENR1-MED.xml new file mode 100644 index 0000000..54482e9 --- /dev/null +++ b/data/0.0.0/images/ENR1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR10-MED.xml b/data/0.0.0/images/ENR10-MED.xml new file mode 100644 index 0000000..dea1acd --- /dev/null +++ b/data/0.0.0/images/ENR10-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR10-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR12-MED.xml b/data/0.0.0/images/ENR12-MED.xml new file mode 100644 index 0000000..82fc8b4 --- /dev/null +++ b/data/0.0.0/images/ENR12-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR12-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR13-MED.xml b/data/0.0.0/images/ENR13-MED.xml new file mode 100644 index 0000000..a25f531 --- /dev/null +++ b/data/0.0.0/images/ENR13-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR13-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR16-MED.xml b/data/0.0.0/images/ENR16-MED.xml new file mode 100644 index 0000000..c7562c3 --- /dev/null +++ b/data/0.0.0/images/ENR16-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR16-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR19-MED.xml b/data/0.0.0/images/ENR19-MED.xml new file mode 100644 index 0000000..4fd1b29 --- /dev/null +++ b/data/0.0.0/images/ENR19-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR19-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR2-MED.xml b/data/0.0.0/images/ENR2-MED.xml new file mode 100644 index 0000000..df04229 --- /dev/null +++ b/data/0.0.0/images/ENR2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR20-MED.xml b/data/0.0.0/images/ENR20-MED.xml new file mode 100644 index 0000000..9c643fd --- /dev/null +++ b/data/0.0.0/images/ENR20-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR20-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR22-MED.xml b/data/0.0.0/images/ENR22-MED.xml new file mode 100644 index 0000000..69fe41e --- /dev/null +++ b/data/0.0.0/images/ENR22-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR22-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR25-MED.xml b/data/0.0.0/images/ENR25-MED.xml new file mode 100644 index 0000000..4d913c7 --- /dev/null +++ b/data/0.0.0/images/ENR25-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR25-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR29-MED.xml b/data/0.0.0/images/ENR29-MED.xml new file mode 100644 index 0000000..7562512 --- /dev/null +++ b/data/0.0.0/images/ENR29-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR29-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR3-MED.xml b/data/0.0.0/images/ENR3-MED.xml new file mode 100644 index 0000000..fd642ca --- /dev/null +++ b/data/0.0.0/images/ENR3-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR3-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR30-MED.xml b/data/0.0.0/images/ENR30-MED.xml new file mode 100644 index 0000000..8ca2cb8 --- /dev/null +++ b/data/0.0.0/images/ENR30-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR30-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR31-MED.xml b/data/0.0.0/images/ENR31-MED.xml new file mode 100644 index 0000000..847756e --- /dev/null +++ b/data/0.0.0/images/ENR31-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR31-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR32-MED.xml b/data/0.0.0/images/ENR32-MED.xml new file mode 100644 index 0000000..94b2474 --- /dev/null +++ b/data/0.0.0/images/ENR32-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR32-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR34-MED.xml b/data/0.0.0/images/ENR34-MED.xml new file mode 100644 index 0000000..ccf0941 --- /dev/null +++ b/data/0.0.0/images/ENR34-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR34-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR39-MED.xml b/data/0.0.0/images/ENR39-MED.xml new file mode 100644 index 0000000..d20e1b7 --- /dev/null +++ b/data/0.0.0/images/ENR39-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR39-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR4-MED.xml b/data/0.0.0/images/ENR4-MED.xml new file mode 100644 index 0000000..e0ab54a --- /dev/null +++ b/data/0.0.0/images/ENR4-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR4-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR46-MED.xml b/data/0.0.0/images/ENR46-MED.xml new file mode 100644 index 0000000..1296b7f --- /dev/null +++ b/data/0.0.0/images/ENR46-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR46-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR54-MED.xml b/data/0.0.0/images/ENR54-MED.xml new file mode 100644 index 0000000..63c34ec --- /dev/null +++ b/data/0.0.0/images/ENR54-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR54-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR57-MED.xml b/data/0.0.0/images/ENR57-MED.xml new file mode 100644 index 0000000..fb1cbed --- /dev/null +++ b/data/0.0.0/images/ENR57-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR57-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR6-MED.xml b/data/0.0.0/images/ENR6-MED.xml new file mode 100644 index 0000000..970400c --- /dev/null +++ b/data/0.0.0/images/ENR6-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR6-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR62-MED.xml b/data/0.0.0/images/ENR62-MED.xml new file mode 100644 index 0000000..f063e2a --- /dev/null +++ b/data/0.0.0/images/ENR62-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR62-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR64-MED.xml b/data/0.0.0/images/ENR64-MED.xml new file mode 100644 index 0000000..b4d3c33 --- /dev/null +++ b/data/0.0.0/images/ENR64-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR64-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR69-MED.xml b/data/0.0.0/images/ENR69-MED.xml new file mode 100644 index 0000000..d175995 --- /dev/null +++ b/data/0.0.0/images/ENR69-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR69-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR71-MED.xml b/data/0.0.0/images/ENR71-MED.xml new file mode 100644 index 0000000..2afb9ab --- /dev/null +++ b/data/0.0.0/images/ENR71-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR71-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR8-MED.xml b/data/0.0.0/images/ENR8-MED.xml new file mode 100644 index 0000000..f658ff8 --- /dev/null +++ b/data/0.0.0/images/ENR8-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR8-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ENR9-MED.xml b/data/0.0.0/images/ENR9-MED.xml new file mode 100644 index 0000000..5da651b --- /dev/null +++ b/data/0.0.0/images/ENR9-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ENR9-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ElaV-MED.xml b/data/0.0.0/images/ElaV-MED.xml new file mode 100644 index 0000000..8ae614b --- /dev/null +++ b/data/0.0.0/images/ElaV-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ElaV-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/FOR-MED.xml b/data/0.0.0/images/FOR-MED.xml new file mode 100644 index 0000000..40c19ab --- /dev/null +++ b/data/0.0.0/images/FOR-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/FOR-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/FVRI-MED.xml b/data/0.0.0/images/FVRI-MED.xml new file mode 100644 index 0000000..e87dc7a --- /dev/null +++ b/data/0.0.0/images/FVRI-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/FVRI-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/FoxD3-MED.xml b/data/0.0.0/images/FoxD3-MED.xml new file mode 100644 index 0000000..0adc27d --- /dev/null +++ b/data/0.0.0/images/FoxD3-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/FoxD3-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/FoxN4-MED.xml b/data/0.0.0/images/FoxN4-MED.xml new file mode 100644 index 0000000..dc91bf1 --- /dev/null +++ b/data/0.0.0/images/FoxN4-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/FoxN4-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GAD-MED.xml b/data/0.0.0/images/GAD-MED.xml new file mode 100644 index 0000000..aeb21c8 --- /dev/null +++ b/data/0.0.0/images/GAD-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GAD-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GCB-MED.xml b/data/0.0.0/images/GCB-MED.xml new file mode 100644 index 0000000..982444b --- /dev/null +++ b/data/0.0.0/images/GCB-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GCB-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GCD-MED.xml b/data/0.0.0/images/GCD-MED.xml new file mode 100644 index 0000000..196b17c --- /dev/null +++ b/data/0.0.0/images/GCD-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GCD-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GPCR2-MED.xml b/data/0.0.0/images/GPCR2-MED.xml new file mode 100644 index 0000000..61bd900 --- /dev/null +++ b/data/0.0.0/images/GPCR2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GPCR2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GPCR203-MED.xml b/data/0.0.0/images/GPCR203-MED.xml new file mode 100644 index 0000000..f2a32cf --- /dev/null +++ b/data/0.0.0/images/GPCR203-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GPCR203-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GPCR209-MED.xml b/data/0.0.0/images/GPCR209-MED.xml new file mode 100644 index 0000000..6fa9945 --- /dev/null +++ b/data/0.0.0/images/GPCR209-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GPCR209-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GPCR210-MED.xml b/data/0.0.0/images/GPCR210-MED.xml new file mode 100644 index 0000000..c21388a --- /dev/null +++ b/data/0.0.0/images/GPCR210-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GPCR210-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GPCR32-MED.xml b/data/0.0.0/images/GPCR32-MED.xml new file mode 100644 index 0000000..b8de6a7 --- /dev/null +++ b/data/0.0.0/images/GPCR32-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GPCR32-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GPPCR21-MED.xml b/data/0.0.0/images/GPPCR21-MED.xml new file mode 100644 index 0000000..2d1fef9 --- /dev/null +++ b/data/0.0.0/images/GPPCR21-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GPPCR21-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Gata123-MED.xml b/data/0.0.0/images/Gata123-MED.xml new file mode 100644 index 0000000..0373a55 --- /dev/null +++ b/data/0.0.0/images/Gata123-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Gata123-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Glt1-MED.xml b/data/0.0.0/images/Glt1-MED.xml new file mode 100644 index 0000000..4b0815d --- /dev/null +++ b/data/0.0.0/images/Glt1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Glt1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GlyT-MED.xml b/data/0.0.0/images/GlyT-MED.xml new file mode 100644 index 0000000..643a8b6 --- /dev/null +++ b/data/0.0.0/images/GlyT-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GlyT-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GnRH-MED.xml b/data/0.0.0/images/GnRH-MED.xml new file mode 100644 index 0000000..586271d --- /dev/null +++ b/data/0.0.0/images/GnRH-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GnRH-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/GnrhR-MED.xml b/data/0.0.0/images/GnrhR-MED.xml new file mode 100644 index 0000000..671c1d7 --- /dev/null +++ b/data/0.0.0/images/GnrhR-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/GnrhR-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Grm7-MED.xml b/data/0.0.0/images/Grm7-MED.xml new file mode 100644 index 0000000..83db30b --- /dev/null +++ b/data/0.0.0/images/Grm7-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Grm7-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Gucy-MED.xml b/data/0.0.0/images/Gucy-MED.xml new file mode 100644 index 0000000..71dd48d --- /dev/null +++ b/data/0.0.0/images/Gucy-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Gucy-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/HCN1-MED.xml b/data/0.0.0/images/HCN1-MED.xml new file mode 100644 index 0000000..de7f8f2 --- /dev/null +++ b/data/0.0.0/images/HCN1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/HCN1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/HNF6-MED.xml b/data/0.0.0/images/HNF6-MED.xml new file mode 100644 index 0000000..1afb59a --- /dev/null +++ b/data/0.0.0/images/HNF6-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/HNF6-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Hand-MED.xml b/data/0.0.0/images/Hand-MED.xml new file mode 100644 index 0000000..993d296 --- /dev/null +++ b/data/0.0.0/images/Hand-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Hand-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Hb9-MED.xml b/data/0.0.0/images/Hb9-MED.xml new file mode 100644 index 0000000..ad107c8 --- /dev/null +++ b/data/0.0.0/images/Hb9-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Hb9-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Hox5-MED.xml b/data/0.0.0/images/Hox5-MED.xml new file mode 100644 index 0000000..59ce6f0 --- /dev/null +++ b/data/0.0.0/images/Hox5-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Hox5-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Hox7-MED.xml b/data/0.0.0/images/Hox7-MED.xml new file mode 100644 index 0000000..9ef95a0 --- /dev/null +++ b/data/0.0.0/images/Hox7-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Hox7-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Hr38-MED.xml b/data/0.0.0/images/Hr38-MED.xml new file mode 100644 index 0000000..2bd5b79 --- /dev/null +++ b/data/0.0.0/images/Hr38-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Hr38-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Isl-MED.xml b/data/0.0.0/images/Isl-MED.xml new file mode 100644 index 0000000..5c22d8e --- /dev/null +++ b/data/0.0.0/images/Isl-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Isl-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Kv33b-MED.xml b/data/0.0.0/images/Kv33b-MED.xml new file mode 100644 index 0000000..6f12dc4 --- /dev/null +++ b/data/0.0.0/images/Kv33b-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Kv33b-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Kv33e-MED.xml b/data/0.0.0/images/Kv33e-MED.xml new file mode 100644 index 0000000..9fa76e3 --- /dev/null +++ b/data/0.0.0/images/Kv33e-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Kv33e-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Lhx15-MED.xml b/data/0.0.0/images/Lhx15-MED.xml new file mode 100644 index 0000000..91aa369 --- /dev/null +++ b/data/0.0.0/images/Lhx15-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Lhx15-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Lhx2-MED.xml b/data/0.0.0/images/Lhx2-MED.xml new file mode 100644 index 0000000..91ec23c --- /dev/null +++ b/data/0.0.0/images/Lhx2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Lhx2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Lhx3-MED.xml b/data/0.0.0/images/Lhx3-MED.xml new file mode 100644 index 0000000..2fa7726 --- /dev/null +++ b/data/0.0.0/images/Lhx3-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Lhx3-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Lmo4-MED.xml b/data/0.0.0/images/Lmo4-MED.xml new file mode 100644 index 0000000..ddbbeb4 --- /dev/null +++ b/data/0.0.0/images/Lmo4-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Lmo4-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Lmx1-MED.xml b/data/0.0.0/images/Lmx1-MED.xml new file mode 100644 index 0000000..d8dcd5c --- /dev/null +++ b/data/0.0.0/images/Lmx1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Lmx1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Loc28250-MED.xml b/data/0.0.0/images/Loc28250-MED.xml new file mode 100644 index 0000000..d68abc3 --- /dev/null +++ b/data/0.0.0/images/Loc28250-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Loc28250-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Loc5285ct-MED.xml b/data/0.0.0/images/Loc5285ct-MED.xml new file mode 100644 index 0000000..43a07d5 --- /dev/null +++ b/data/0.0.0/images/Loc5285ct-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Loc5285ct-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Loc77859-MED.xml b/data/0.0.0/images/Loc77859-MED.xml new file mode 100644 index 0000000..384e48b --- /dev/null +++ b/data/0.0.0/images/Loc77859-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Loc77859-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Loc8913nt-MED.xml b/data/0.0.0/images/Loc8913nt-MED.xml new file mode 100644 index 0000000..0e2d87c --- /dev/null +++ b/data/0.0.0/images/Loc8913nt-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Loc8913nt-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/MHCL4-MED.xml b/data/0.0.0/images/MHCL4-MED.xml new file mode 100644 index 0000000..490a9c0 --- /dev/null +++ b/data/0.0.0/images/MHCL4-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/MHCL4-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/MRLC2-MED.xml b/data/0.0.0/images/MRLC2-MED.xml new file mode 100644 index 0000000..6e1a117 --- /dev/null +++ b/data/0.0.0/images/MRLC2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/MRLC2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Maf-MED.xml b/data/0.0.0/images/Maf-MED.xml new file mode 100644 index 0000000..41bdf58 --- /dev/null +++ b/data/0.0.0/images/Maf-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Maf-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Mitf-MED.xml b/data/0.0.0/images/Mitf-MED.xml new file mode 100644 index 0000000..7b2d1e8 --- /dev/null +++ b/data/0.0.0/images/Mitf-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Mitf-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Munc22-MED.xml b/data/0.0.0/images/Munc22-MED.xml new file mode 100644 index 0000000..b06523c --- /dev/null +++ b/data/0.0.0/images/Munc22-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Munc22-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NMDAR-MED.xml b/data/0.0.0/images/NMDAR-MED.xml new file mode 100644 index 0000000..7ce2b29 --- /dev/null +++ b/data/0.0.0/images/NMDAR-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NMDAR-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NOV1-MED.xml b/data/0.0.0/images/NOV1-MED.xml new file mode 100644 index 0000000..e1ee107 --- /dev/null +++ b/data/0.0.0/images/NOV1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NOV1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NOV15-MED.xml b/data/0.0.0/images/NOV15-MED.xml new file mode 100644 index 0000000..8eb1f23 --- /dev/null +++ b/data/0.0.0/images/NOV15-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NOV15-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NOV18-MED.xml b/data/0.0.0/images/NOV18-MED.xml new file mode 100644 index 0000000..c72cbcb --- /dev/null +++ b/data/0.0.0/images/NOV18-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NOV18-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NOV2-MED.xml b/data/0.0.0/images/NOV2-MED.xml new file mode 100644 index 0000000..e0f6757 --- /dev/null +++ b/data/0.0.0/images/NOV2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NOV2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NOV29-MED.xml b/data/0.0.0/images/NOV29-MED.xml new file mode 100644 index 0000000..24a2ebc --- /dev/null +++ b/data/0.0.0/images/NOV29-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NOV29-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NOV45-MED.xml b/data/0.0.0/images/NOV45-MED.xml new file mode 100644 index 0000000..0a99807 --- /dev/null +++ b/data/0.0.0/images/NOV45-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NOV45-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NOV50-MED.xml b/data/0.0.0/images/NOV50-MED.xml new file mode 100644 index 0000000..f134e84 --- /dev/null +++ b/data/0.0.0/images/NOV50-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NOV50-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NOV52-MED.xml b/data/0.0.0/images/NOV52-MED.xml new file mode 100644 index 0000000..db0e4a1 --- /dev/null +++ b/data/0.0.0/images/NOV52-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NOV52-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NOV6-MED.xml b/data/0.0.0/images/NOV6-MED.xml new file mode 100644 index 0000000..69b2c97 --- /dev/null +++ b/data/0.0.0/images/NOV6-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NOV6-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NPR1a-MED.xml b/data/0.0.0/images/NPR1a-MED.xml new file mode 100644 index 0000000..2f3420f --- /dev/null +++ b/data/0.0.0/images/NPR1a-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NPR1a-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Netrin-MED.xml b/data/0.0.0/images/Netrin-MED.xml new file mode 100644 index 0000000..f0dc724 --- /dev/null +++ b/data/0.0.0/images/Netrin-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Netrin-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/NeuroD-MED.xml b/data/0.0.0/images/NeuroD-MED.xml new file mode 100644 index 0000000..f6fe565 --- /dev/null +++ b/data/0.0.0/images/NeuroD-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/NeuroD-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Ngb-MED.xml b/data/0.0.0/images/Ngb-MED.xml new file mode 100644 index 0000000..d4ad71e --- /dev/null +++ b/data/0.0.0/images/Ngb-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Ngb-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Olig-MED.xml b/data/0.0.0/images/Olig-MED.xml new file mode 100644 index 0000000..8ff3f9d --- /dev/null +++ b/data/0.0.0/images/Olig-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Olig-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/P56-MED.xml b/data/0.0.0/images/P56-MED.xml new file mode 100644 index 0000000..bd30c75 --- /dev/null +++ b/data/0.0.0/images/P56-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/P56-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/PCDH15-MED.xml b/data/0.0.0/images/PCDH15-MED.xml new file mode 100644 index 0000000..3612649 --- /dev/null +++ b/data/0.0.0/images/PCDH15-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/PCDH15-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/PDF-MED.xml b/data/0.0.0/images/PDF-MED.xml new file mode 100644 index 0000000..4653614 --- /dev/null +++ b/data/0.0.0/images/PDF-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/PDF-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/PLCg-MED.xml b/data/0.0.0/images/PLCg-MED.xml new file mode 100644 index 0000000..c6ea997 --- /dev/null +++ b/data/0.0.0/images/PLCg-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/PLCg-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Pax258-MED.xml b/data/0.0.0/images/Pax258-MED.xml new file mode 100644 index 0000000..eeb0228 --- /dev/null +++ b/data/0.0.0/images/Pax258-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Pax258-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Pax6-MED.xml b/data/0.0.0/images/Pax6-MED.xml new file mode 100644 index 0000000..6338e58 --- /dev/null +++ b/data/0.0.0/images/Pax6-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Pax6-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Pde9-MED.xml b/data/0.0.0/images/Pde9-MED.xml new file mode 100644 index 0000000..c1c629b --- /dev/null +++ b/data/0.0.0/images/Pde9-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Pde9-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Pea3-MED.xml b/data/0.0.0/images/Pea3-MED.xml new file mode 100644 index 0000000..ec0d587 --- /dev/null +++ b/data/0.0.0/images/Pea3-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Pea3-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Phc2-MED.xml b/data/0.0.0/images/Phc2-MED.xml new file mode 100644 index 0000000..b107fcb --- /dev/null +++ b/data/0.0.0/images/Phc2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Phc2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Phox2b-MED.xml b/data/0.0.0/images/Phox2b-MED.xml new file mode 100644 index 0000000..ba7a484 --- /dev/null +++ b/data/0.0.0/images/Phox2b-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Phox2b-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Pikachu-MED.xml b/data/0.0.0/images/Pikachu-MED.xml new file mode 100644 index 0000000..5d8c93a --- /dev/null +++ b/data/0.0.0/images/Pikachu-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Pikachu-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/PitxB-MED.xml b/data/0.0.0/images/PitxB-MED.xml new file mode 100644 index 0000000..9a4a842 --- /dev/null +++ b/data/0.0.0/images/PitxB-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/PitxB-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Prdm8-MED.xml b/data/0.0.0/images/Prdm8-MED.xml new file mode 100644 index 0000000..3f8eb25 --- /dev/null +++ b/data/0.0.0/images/Prdm8-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Prdm8-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Prox-MED.xml b/data/0.0.0/images/Prox-MED.xml new file mode 100644 index 0000000..e80c888 --- /dev/null +++ b/data/0.0.0/images/Prox-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Prox-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Ptf1-MED.xml b/data/0.0.0/images/Ptf1-MED.xml new file mode 100644 index 0000000..6373cda --- /dev/null +++ b/data/0.0.0/images/Ptf1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Ptf1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Pty2-MED.xml b/data/0.0.0/images/Pty2-MED.xml new file mode 100644 index 0000000..c5b9151 --- /dev/null +++ b/data/0.0.0/images/Pty2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Pty2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/RIMS-MED.xml b/data/0.0.0/images/RIMS-MED.xml new file mode 100644 index 0000000..65b77a2 --- /dev/null +++ b/data/0.0.0/images/RIMS-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/RIMS-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Rab3-MED.xml b/data/0.0.0/images/Rab3-MED.xml new file mode 100644 index 0000000..12bbb91 --- /dev/null +++ b/data/0.0.0/images/Rab3-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Rab3-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Robo-MED.xml b/data/0.0.0/images/Robo-MED.xml new file mode 100644 index 0000000..ba73c5d --- /dev/null +++ b/data/0.0.0/images/Robo-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Robo-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Scn8aa-MED.xml b/data/0.0.0/images/Scn8aa-MED.xml new file mode 100644 index 0000000..dd84f38 --- /dev/null +++ b/data/0.0.0/images/Scn8aa-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Scn8aa-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Sema2-MED.xml b/data/0.0.0/images/Sema2-MED.xml new file mode 100644 index 0000000..6c2a9e1 --- /dev/null +++ b/data/0.0.0/images/Sema2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Sema2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Sim1-MED.xml b/data/0.0.0/images/Sim1-MED.xml new file mode 100644 index 0000000..ea5c570 --- /dev/null +++ b/data/0.0.0/images/Sim1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Sim1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Slit-MED.xml b/data/0.0.0/images/Slit-MED.xml new file mode 100644 index 0000000..bcebb90 --- /dev/null +++ b/data/0.0.0/images/Slit-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Slit-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Sox2-MED.xml b/data/0.0.0/images/Sox2-MED.xml new file mode 100644 index 0000000..d6e72df --- /dev/null +++ b/data/0.0.0/images/Sox2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Sox2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Sox4-MED.xml b/data/0.0.0/images/Sox4-MED.xml new file mode 100644 index 0000000..5aa36b1 --- /dev/null +++ b/data/0.0.0/images/Sox4-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Sox4-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/SoxB12-MED.xml b/data/0.0.0/images/SoxB12-MED.xml new file mode 100644 index 0000000..31ec3f9 --- /dev/null +++ b/data/0.0.0/images/SoxB12-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/SoxB12-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/SoxB2-MED.xml b/data/0.0.0/images/SoxB2-MED.xml new file mode 100644 index 0000000..9dd3c01 --- /dev/null +++ b/data/0.0.0/images/SoxB2-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/SoxB2-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Sp8-MED.xml b/data/0.0.0/images/Sp8-MED.xml new file mode 100644 index 0000000..9391508 --- /dev/null +++ b/data/0.0.0/images/Sp8-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Sp8-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Syt-MED.xml b/data/0.0.0/images/Syt-MED.xml new file mode 100644 index 0000000..f2325e4 --- /dev/null +++ b/data/0.0.0/images/Syt-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Syt-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Syt12-MED.xml b/data/0.0.0/images/Syt12-MED.xml new file mode 100644 index 0000000..695b1e9 --- /dev/null +++ b/data/0.0.0/images/Syt12-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Syt12-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Syt7-MED.xml b/data/0.0.0/images/Syt7-MED.xml new file mode 100644 index 0000000..0b704c1 --- /dev/null +++ b/data/0.0.0/images/Syt7-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Syt7-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Syta-MED.xml b/data/0.0.0/images/Syta-MED.xml new file mode 100644 index 0000000..bd0e0e8 --- /dev/null +++ b/data/0.0.0/images/Syta-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Syta-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/TH-MED.xml b/data/0.0.0/images/TH-MED.xml new file mode 100644 index 0000000..a49831a --- /dev/null +++ b/data/0.0.0/images/TH-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/TH-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/TIMP-MED.xml b/data/0.0.0/images/TIMP-MED.xml new file mode 100644 index 0000000..a3836d3 --- /dev/null +++ b/data/0.0.0/images/TIMP-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/TIMP-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/TRPV4-MED.xml b/data/0.0.0/images/TRPV4-MED.xml new file mode 100644 index 0000000..8660000 --- /dev/null +++ b/data/0.0.0/images/TRPV4-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/TRPV4-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/TRPV5-MED.xml b/data/0.0.0/images/TRPV5-MED.xml new file mode 100644 index 0000000..2e2b25a --- /dev/null +++ b/data/0.0.0/images/TRPV5-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/TRPV5-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Tal-MED.xml b/data/0.0.0/images/Tal-MED.xml new file mode 100644 index 0000000..47d2ec1 --- /dev/null +++ b/data/0.0.0/images/Tal-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Tal-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Tbh-MED.xml b/data/0.0.0/images/Tbh-MED.xml new file mode 100644 index 0000000..ee6f9ea --- /dev/null +++ b/data/0.0.0/images/Tbh-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Tbh-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Tbx20-MED.xml b/data/0.0.0/images/Tbx20-MED.xml new file mode 100644 index 0000000..a6aed88 --- /dev/null +++ b/data/0.0.0/images/Tbx20-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Tbx20-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/TrpH-MED.xml b/data/0.0.0/images/TrpH-MED.xml new file mode 100644 index 0000000..2717552 --- /dev/null +++ b/data/0.0.0/images/TrpH-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/TrpH-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/TrpV-MED.xml b/data/0.0.0/images/TrpV-MED.xml new file mode 100644 index 0000000..4541f06 --- /dev/null +++ b/data/0.0.0/images/TrpV-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/TrpV-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Twist-MED.xml b/data/0.0.0/images/Twist-MED.xml new file mode 100644 index 0000000..6993b15 --- /dev/null +++ b/data/0.0.0/images/Twist-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Twist-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/UNCS-MED.xml b/data/0.0.0/images/UNCS-MED.xml new file mode 100644 index 0000000..b4324b3 --- /dev/null +++ b/data/0.0.0/images/UNCS-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/UNCS-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/VAChT-MED.xml b/data/0.0.0/images/VAChT-MED.xml new file mode 100644 index 0000000..59c3ab5 --- /dev/null +++ b/data/0.0.0/images/VAChT-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/VAChT-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/VAT1L-MED.xml b/data/0.0.0/images/VAT1L-MED.xml new file mode 100644 index 0000000..d665a55 --- /dev/null +++ b/data/0.0.0/images/VAT1L-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/VAT1L-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/VGluT-MED.xml b/data/0.0.0/images/VGluT-MED.xml new file mode 100644 index 0000000..ba12fa4 --- /dev/null +++ b/data/0.0.0/images/VGluT-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/VGluT-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/VegfR-MED.xml b/data/0.0.0/images/VegfR-MED.xml new file mode 100644 index 0000000..6839f9a --- /dev/null +++ b/data/0.0.0/images/VegfR-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/VegfR-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Wnt16-MED.xml b/data/0.0.0/images/Wnt16-MED.xml new file mode 100644 index 0000000..43a2e24 --- /dev/null +++ b/data/0.0.0/images/Wnt16-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Wnt16-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/Wnt5-MED.xml b/data/0.0.0/images/Wnt5-MED.xml new file mode 100644 index 0000000..d7ffa2e --- /dev/null +++ b/data/0.0.0/images/Wnt5-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/Wnt5-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ascI-MED.xml b/data/0.0.0/images/ascI-MED.xml new file mode 100644 index 0000000..5f85db3 --- /dev/null +++ b/data/0.0.0/images/ascI-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ascI-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ascII-MED.xml b/data/0.0.0/images/ascII-MED.xml new file mode 100644 index 0000000..f2b2bfb --- /dev/null +++ b/data/0.0.0/images/ascII-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ascII-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/asicalpha-MED.xml b/data/0.0.0/images/asicalpha-MED.xml new file mode 100644 index 0000000..2f536fa --- /dev/null +++ b/data/0.0.0/images/asicalpha-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/asicalpha-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/bsx-MED.xml b/data/0.0.0/images/bsx-MED.xml new file mode 100644 index 0000000..5d97315 --- /dev/null +++ b/data/0.0.0/images/bsx-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/bsx-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/catL-MED.xml b/data/0.0.0/images/catL-MED.xml new file mode 100644 index 0000000..f11fc0f --- /dev/null +++ b/data/0.0.0/images/catL-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/catL-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/cnga-MED.xml b/data/0.0.0/images/cnga-MED.xml new file mode 100644 index 0000000..7fb999d --- /dev/null +++ b/data/0.0.0/images/cnga-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/cnga-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/dbx1-MED.xml b/data/0.0.0/images/dbx1-MED.xml new file mode 100644 index 0000000..83c6e68 --- /dev/null +++ b/data/0.0.0/images/dbx1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/dbx1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/delta-MED.xml b/data/0.0.0/images/delta-MED.xml new file mode 100644 index 0000000..903c11d --- /dev/null +++ b/data/0.0.0/images/delta-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/delta-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/dlx-MED.xml b/data/0.0.0/images/dlx-MED.xml new file mode 100644 index 0000000..fc5fff1 --- /dev/null +++ b/data/0.0.0/images/dlx-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/dlx-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/edu3to4at6dpf-MED.xml b/data/0.0.0/images/edu3to4at6dpf-MED.xml new file mode 100644 index 0000000..0755eb7 --- /dev/null +++ b/data/0.0.0/images/edu3to4at6dpf-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/edu3to4at6dpf-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/edu4to5at6dpf-MED.xml b/data/0.0.0/images/edu4to5at6dpf-MED.xml new file mode 100644 index 0000000..25b8700 --- /dev/null +++ b/data/0.0.0/images/edu4to5at6dpf-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/edu4to5at6dpf-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/edu5to6at6dpf-MED.xml b/data/0.0.0/images/edu5to6at6dpf-MED.xml new file mode 100644 index 0000000..ac57b3e --- /dev/null +++ b/data/0.0.0/images/edu5to6at6dpf-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/edu5to6at6dpf-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/eve-MED.xml b/data/0.0.0/images/eve-MED.xml new file mode 100644 index 0000000..b58cce2 --- /dev/null +++ b/data/0.0.0/images/eve-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/eve-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/eya-MED.xml b/data/0.0.0/images/eya-MED.xml new file mode 100644 index 0000000..832bcee --- /dev/null +++ b/data/0.0.0/images/eya-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/eya-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/fezf-MED.xml b/data/0.0.0/images/fezf-MED.xml new file mode 100644 index 0000000..ac2d24f --- /dev/null +++ b/data/0.0.0/images/fezf-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/fezf-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/gpb-MED.xml b/data/0.0.0/images/gpb-MED.xml new file mode 100644 index 0000000..029497a --- /dev/null +++ b/data/0.0.0/images/gpb-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/gpb-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/gsx-MED.xml b/data/0.0.0/images/gsx-MED.xml new file mode 100644 index 0000000..27c2b13 --- /dev/null +++ b/data/0.0.0/images/gsx-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/gsx-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/hox1-MED.xml b/data/0.0.0/images/hox1-MED.xml new file mode 100644 index 0000000..d4701bf --- /dev/null +++ b/data/0.0.0/images/hox1-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/hox1-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/irx-MED.xml b/data/0.0.0/images/irx-MED.xml new file mode 100644 index 0000000..d048c8a --- /dev/null +++ b/data/0.0.0/images/irx-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/irx-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/irx2546-MED.xml b/data/0.0.0/images/irx2546-MED.xml new file mode 100644 index 0000000..9d99a97 --- /dev/null +++ b/data/0.0.0/images/irx2546-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/irx2546-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/lbx1b-MED.xml b/data/0.0.0/images/lbx1b-MED.xml new file mode 100644 index 0000000..5b9a1ef --- /dev/null +++ b/data/0.0.0/images/lbx1b-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/lbx1b-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/lhx6-MED.xml b/data/0.0.0/images/lhx6-MED.xml new file mode 100644 index 0000000..c1aa7e0 --- /dev/null +++ b/data/0.0.0/images/lhx6-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/lhx6-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/mecom-MED.xml b/data/0.0.0/images/mecom-MED.xml new file mode 100644 index 0000000..04aaa09 --- /dev/null +++ b/data/0.0.0/images/mecom-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/mecom-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/msx-MED.xml b/data/0.0.0/images/msx-MED.xml new file mode 100644 index 0000000..a3dad76 --- /dev/null +++ b/data/0.0.0/images/msx-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/msx-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/muncB-MED.xml b/data/0.0.0/images/muncB-MED.xml new file mode 100644 index 0000000..3dea2b6 --- /dev/null +++ b/data/0.0.0/images/muncB-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/muncB-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/nAchR-MED.xml b/data/0.0.0/images/nAchR-MED.xml new file mode 100644 index 0000000..5cef7db --- /dev/null +++ b/data/0.0.0/images/nAchR-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/nAchR-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/neog-MED.xml b/data/0.0.0/images/neog-MED.xml new file mode 100644 index 0000000..9ffc62a --- /dev/null +++ b/data/0.0.0/images/neog-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/neog-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ngn-MED.xml b/data/0.0.0/images/ngn-MED.xml new file mode 100644 index 0000000..7a076e6 --- /dev/null +++ b/data/0.0.0/images/ngn-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ngn-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/nk21-MED.xml b/data/0.0.0/images/nk21-MED.xml new file mode 100644 index 0000000..de2cfa8 --- /dev/null +++ b/data/0.0.0/images/nk21-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/nk21-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/nk22-MED.xml b/data/0.0.0/images/nk22-MED.xml new file mode 100644 index 0000000..638a2d7 --- /dev/null +++ b/data/0.0.0/images/nk22-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/nk22-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/nk6-MED.xml b/data/0.0.0/images/nk6-MED.xml new file mode 100644 index 0000000..61f685b --- /dev/null +++ b/data/0.0.0/images/nk6-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/nk6-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/ntrps-MED.xml b/data/0.0.0/images/ntrps-MED.xml new file mode 100644 index 0000000..97008e8 --- /dev/null +++ b/data/0.0.0/images/ntrps-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/ntrps-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/otp-MED.xml b/data/0.0.0/images/otp-MED.xml new file mode 100644 index 0000000..11f344b --- /dev/null +++ b/data/0.0.0/images/otp-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/otp-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/paraxis-MED.xml b/data/0.0.0/images/paraxis-MED.xml new file mode 100644 index 0000000..bf22f8c --- /dev/null +++ b/data/0.0.0/images/paraxis-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/paraxis-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/rx-MED.xml b/data/0.0.0/images/rx-MED.xml new file mode 100644 index 0000000..5e6e562 --- /dev/null +++ b/data/0.0.0/images/rx-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/rx-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/sert-MED.xml b/data/0.0.0/images/sert-MED.xml new file mode 100644 index 0000000..1d6d6d9 --- /dev/null +++ b/data/0.0.0/images/sert-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/sert-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/six12-MED.xml b/data/0.0.0/images/six12-MED.xml new file mode 100644 index 0000000..9333f20 --- /dev/null +++ b/data/0.0.0/images/six12-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/six12-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/six4-MED.xml b/data/0.0.0/images/six4-MED.xml new file mode 100644 index 0000000..3194b5b --- /dev/null +++ b/data/0.0.0/images/six4-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/six4-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/tlx-MED.xml b/data/0.0.0/images/tlx-MED.xml new file mode 100644 index 0000000..d3b7620 --- /dev/null +++ b/data/0.0.0/images/tlx-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/tlx-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/trk-MED.xml b/data/0.0.0/images/trk-MED.xml new file mode 100644 index 0000000..2133928 --- /dev/null +++ b/data/0.0.0/images/trk-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/trk-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/data/0.0.0/images/uncx-MED.xml b/data/0.0.0/images/uncx-MED.xml new file mode 100644 index 0000000..9755545 --- /dev/null +++ b/data/0.0.0/images/uncx-MED.xml @@ -0,0 +1,39 @@ +<SpimData version="0.2"> + <BasePath type="relative">.</BasePath> + <SequenceDescription> + <ImageLoader format="bdv.hdf5"> + <hdf5 type="absolute">/g/arendt/EM_6dpf_segmentation/EM-Prospr/uncx-MED.h5</hdf5> + </ImageLoader> + <ViewSetups> + <ViewSetup> + <id>0</id> + <name>channel 1</name> + <size>550 518 570</size> + <voxelSize> + <unit>micrometer</unit> + <size>0.5 0.5 0.5</size> + </voxelSize> + <attributes> + <channel>1</channel> + </attributes> + </ViewSetup> + <Attributes name="channel"> + <Channel> + <id>1</id> + <name>1</name> + </Channel> + </Attributes> + </ViewSetups> + <Timepoints type="range"> + <first>0</first> + <last>0</last> + </Timepoints> + </SequenceDescription> + <ViewRegistrations> + <ViewRegistration setup="0" timepoint="0"> + <ViewTransform type="affine"> + <affine>0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0</affine> + </ViewTransform> + </ViewRegistration> + </ViewRegistrations> +</SpimData> diff --git a/make_initial_version.py b/make_initial_version.py index 67e39e0..8bf33d5 100755 --- a/make_initial_version.py +++ b/make_initial_version.py @@ -6,6 +6,7 @@ from shutil import copyfile from scripts.files import make_folder_structure from scripts.export import export_segmentation from scripts.files import copy_xml_with_abspath, write_simple_xml +from scripts.files import copy_files_with_pattern from scripts.attributes import make_nucleus_tables, make_cell_tables @@ -44,13 +45,18 @@ def make_image_data(old_folder, folder): raw_out = os.path.join(data_folder, raw_name) copy_xml_with_abspath(raw_in, raw_out) + # TODO sub-folder ? + # copy MEDs and SPMs + copy_files_with_pattern(old_folder, data_folder, "*-MED*") + # TODO do we need the SPMs here? + # copy_files_with_pattern(old_folder, data_folder, "*-SPM*") + # copy valentyna's aux gene file misc_folder = os.path.join(folder, 'misc') copy_aux_gene_file(misc_folder) - # TODO - # copy MEDs and SPMs # copy cellular models + # TODO # copy additional segmentations # (muscle, tissue (includes neuropil), TODO more?) diff --git a/scripts/files/__init__.py b/scripts/files/__init__.py index b7f0b02..5088d2a 100644 --- a/scripts/files/__init__.py +++ b/scripts/files/__init__.py @@ -1,3 +1,4 @@ from .copy_helper import copy_tables, copy_segmentation, copy_static_files +from .copy_helper import copy_files_with_pattern from .folders import make_folder_structure from .xml_utils import get_h5_path_from_xml, copy_xml_with_abspath, write_simple_xml diff --git a/scripts/files/copy_helper.py b/scripts/files/copy_helper.py index e34ae38..13a32c9 100644 --- a/scripts/files/copy_helper.py +++ b/scripts/files/copy_helper.py @@ -1,4 +1,18 @@ import os +import glob +from .xml_utils import copy_xml_with_abspath + + +def copy_files_with_pattern(src_folder, dst_folder, pattern): + files = glob.glob(os.path.join(src_folder, pattern)) + for ff in files: + ext = os.path.splitext(ff)[1] + if ext != '.xml': + continue + xml_in = ff + xml_out = os.path.join(dst_folder, + os.path.split(ff)[1]) + copy_xml_with_abspath(xml_in, xml_out) def copy_tables(src_folder, dst_folder, name): -- GitLab