From 18e01d15161dd8738675ce287bda59f3c25cb5a9 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Fri, 30 Aug 2019 13:15:26 +0200
Subject: [PATCH] Update patch version
---
.../images/prospr-6dpf-1-whole-AChE-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ANPRA-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ANPRB-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-AP2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ASCb-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-AcTub-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-AllCR1-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-AllCR2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Arx-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Ash-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-BAIAP-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-BarH1-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Beta3-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Bmpr1-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Brn3a-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-COE-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Cal2-MED.xml | 39 ++
.../prospr-6dpf-1-whole-Calmodulin-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ChAT-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Chx10-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Dach-MED.xml | 39 ++
.../prospr-6dpf-1-whole-DbhLike-MED.xml | 39 ++
.../prospr-6dpf-1-whole-DopaRD2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR1-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR10-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR12-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR13-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR16-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR19-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR20-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR22-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR25-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR29-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR3-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR30-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR31-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR32-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR34-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR39-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR4-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR46-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR54-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR57-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR6-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR62-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR64-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR69-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR71-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR8-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ENR9-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ElaV-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-FOR-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-FVRI-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-FoxD3-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-FoxN4-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-GAD-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-GCB-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-GCD-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-GPCR2-MED.xml | 39 ++
.../prospr-6dpf-1-whole-GPCR203-MED.xml | 39 ++
.../prospr-6dpf-1-whole-GPCR209-MED.xml | 39 ++
.../prospr-6dpf-1-whole-GPCR210-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-GPCR32-MED.xml | 39 ++
.../prospr-6dpf-1-whole-GPPCR21-MED.xml | 39 ++
.../prospr-6dpf-1-whole-Gata123-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Glt1-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-GlyT-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-GnRH-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-GnrhR-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Grm7-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Gucy-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-HCN1-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-HNF6-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Hand-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Hb9-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Hox5-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Hox7-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Hr38-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Isl-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Kv33b-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Kv33e-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Lhx15-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Lhx2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Lhx3-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Lmo4-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Lmx1-MED.xml | 39 ++
.../prospr-6dpf-1-whole-Loc28250-MED.xml | 39 ++
.../prospr-6dpf-1-whole-Loc5285ct-MED.xml | 39 ++
.../prospr-6dpf-1-whole-Loc77859-MED.xml | 39 ++
.../prospr-6dpf-1-whole-Loc8913nt-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-MHCL4-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-MRLC2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Maf-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Mitf-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Munc22-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NMDAR-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NOV1-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NOV15-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NOV18-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NOV2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NOV29-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NOV45-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NOV50-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NOV52-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NOV6-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NPR1a-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Netrin-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-NeuroD-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Ngb-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Olig-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-P56-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-PCDH15-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-PDF-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-PLCg-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Pax258-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Pax6-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Pde9-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Pea3-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Phc2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Phox2b-MED.xml | 39 ++
.../prospr-6dpf-1-whole-Pikachu-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-PitxB-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Prdm8-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Prox-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Ptf1-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Pty2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-RIMS-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Rab3-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Robo-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Scn8aa-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Sema2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Sim1-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Slit-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Sox2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Sox4-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-SoxB12-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-SoxB2-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Sp8-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Syt-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Syt12-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Syt7-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Syta-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-TH-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-TIMP-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-TRPV4-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-TRPV5-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Tal-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Tbh-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Tbx20-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-TrpH-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-TrpV-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Twist-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-UNCS-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-VAChT-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-VAT1L-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-VGluT-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-VegfR-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Wnt16-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-Wnt5-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ascI-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ascII-MED.xml | 39 ++
.../prospr-6dpf-1-whole-asicalpha-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-bsx-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-catL-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-cnga-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-dbx1-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-delta-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-dlx-MED.xml | 39 ++
.../prospr-6dpf-1-whole-edu3to4at6dpf-MED.xml | 39 ++
.../prospr-6dpf-1-whole-edu4to5at6dpf-MED.xml | 39 ++
.../prospr-6dpf-1-whole-edu5to6at6dpf-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-eve-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-eya-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-fezf-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-gpb-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-gsx-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-hox1-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-irx-MED.xml | 39 ++
.../prospr-6dpf-1-whole-irx2546-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-lbx1b-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-lhx6-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-mecom-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-msx-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-muncB-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-nAchR-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-neog-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ngn-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-nk21-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-nk22-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-nk6-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ntrps-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-otp-MED.xml | 39 ++
.../prospr-6dpf-1-whole-paraxis-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-ref-SPM.xml | 39 ++
.../images/prospr-6dpf-1-whole-rx-MED.xml | 39 ++
...-6dpf-1-whole-segmented-CrypticSegment.xml | 39 ++
.../prospr-6dpf-1-whole-segmented-Head.xml | 39 ++
.../prospr-6dpf-1-whole-segmented-PNS.xml | 39 ++
...prospr-6dpf-1-whole-segmented-Pygidium.xml | 39 ++
...pr-6dpf-1-whole-segmented-RestOfAnimal.xml | 39 ++
...rospr-6dpf-1-whole-segmented-Stomodeum.xml | 39 ++
.../prospr-6dpf-1-whole-segmented-VNC.xml | 39 ++
.../images/prospr-6dpf-1-whole-sert-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-six12-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-six4-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-tlx-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-trk-MED.xml | 39 ++
.../images/prospr-6dpf-1-whole-uncx-MED.xml | 39 ++
.../images/sbem-6dpf-1-whole-mask-inside.xml | 39 ++
.../images/sbem-6dpf-1-whole-mask-outside.xml | 39 ++
.../images/sbem-6dpf-1-whole-mask-resin.xml | 39 ++
data/0.5.1/images/sbem-6dpf-1-whole-raw.xml | 39 ++
data/0.5.1/misc/bdv_server.txt | 221 ++++++++
data/0.5.1/misc/bookmarks.json | 6 +
data/0.5.1/misc/cilia_id_mapping.csv | 125 ++++
...m-6dpf-1-whole-segmented-cells-labels.json | 1 +
...m-6dpf-1-whole-segmented-cilia-labels.json | 1 +
...-6dpf-1-whole-segmented-nuclei-labels.json | 1 +
.../prospr-6dpf-1-whole_meds_all_genes.xml | 8 +
...dpf-1-whole-segmented-ariande-neuropil.xml | 39 ++
...m-6dpf-1-whole-segmented-cats-neuropil.xml | 39 ++
...em-6dpf-1-whole-segmented-cells-labels.xml | 39 ++
...dpf-1-whole-segmented-chromatin-labels.xml | 39 ++
...em-6dpf-1-whole-segmented-cilia-labels.xml | 39 ++
.../sbem-6dpf-1-whole-segmented-muscle.xml | 39 ++
...m-6dpf-1-whole-segmented-nuclei-labels.xml | 39 ++
...m-6dpf-1-whole-segmented-tissue-labels.xml | 39 ++
.../sbem-6dpf-1-whole-traces-labels.xml | 39 ++
.../cells_to_nuclei.csv | 1 +
.../default.csv | 1 +
.../genes.csv | 1 +
.../morphology.csv | 1 +
.../regions.csv | 1 +
.../default.csv | 1 +
.../cilia.csv | 533 ++++++++++++++++++
.../default.csv | 533 ++++++++++++++++++
.../default.csv.bkp | 533 ++++++++++++++++++
.../default.csv | 1 +
.../morphology.csv | 1 +
.../default.csv | 1 +
.../default.csv | 1 +
data/versions.json | 2 +-
scripts/attributes/cilia_attributes.py | 70 +++
scripts/attributes/master.py | 16 +-
245 files changed, 10715 insertions(+), 3 deletions(-)
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-AChE-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ANPRA-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ANPRB-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-AP2-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ASCb-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-AcTub-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-AllCR1-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-AllCR2-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Arx-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Ash-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-BAIAP-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-BarH1-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Beta3-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Bmpr1-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Brn3a-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-COE-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Cal2-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Calmodulin-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ChAT-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Chx10-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Dach-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-DbhLike-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-DopaRD2-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR1-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR10-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR12-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR13-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR16-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR19-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR2-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR20-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR22-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR25-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR29-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR3-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR30-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR31-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR32-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR34-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR39-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR4-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR46-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR54-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR57-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR6-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR62-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR64-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR69-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR71-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR8-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ENR9-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ElaV-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-FOR-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-FVRI-MED.xml
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create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-PCDH15-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-PDF-MED.xml
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create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Phox2b-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Pikachu-MED.xml
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create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Slit-MED.xml
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create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Sox4-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-SoxB12-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-SoxB2-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Sp8-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Syt-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Syt12-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Syt7-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Syta-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-TH-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-TIMP-MED.xml
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create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-TRPV5-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Tal-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Tbh-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Tbx20-MED.xml
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create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-TrpV-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Twist-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-UNCS-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-VAChT-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-VAT1L-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-VGluT-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-VegfR-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Wnt16-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-Wnt5-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ascI-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ascII-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-asicalpha-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-bsx-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-catL-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-cnga-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-dbx1-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-delta-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-dlx-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-edu3to4at6dpf-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-edu4to5at6dpf-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-edu5to6at6dpf-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-eve-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-eya-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-fezf-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-gpb-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-gsx-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-hox1-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-irx-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-irx2546-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-lbx1b-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-lhx6-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-mecom-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-msx-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-muncB-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-nAchR-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-neog-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ngn-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-nk21-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-nk22-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-nk6-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ntrps-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-otp-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-paraxis-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-ref-SPM.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-rx-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-segmented-CrypticSegment.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-segmented-Head.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-segmented-PNS.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-segmented-Pygidium.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-segmented-RestOfAnimal.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-segmented-Stomodeum.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-segmented-VNC.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-sert-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-six12-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-six4-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-tlx-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-trk-MED.xml
create mode 100644 data/0.5.1/images/prospr-6dpf-1-whole-uncx-MED.xml
create mode 100644 data/0.5.1/images/sbem-6dpf-1-whole-mask-inside.xml
create mode 100644 data/0.5.1/images/sbem-6dpf-1-whole-mask-outside.xml
create mode 100644 data/0.5.1/images/sbem-6dpf-1-whole-mask-resin.xml
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create mode 100644 data/0.5.1/misc/bdv_server.txt
create mode 100644 data/0.5.1/misc/bookmarks.json
create mode 100644 data/0.5.1/misc/cilia_id_mapping.csv
create mode 120000 data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-cells-labels.json
create mode 100644 data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-cilia-labels.json
create mode 120000 data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-nuclei-labels.json
create mode 100644 data/0.5.1/misc/prospr-6dpf-1-whole_meds_all_genes.xml
create mode 100644 data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-ariande-neuropil.xml
create mode 100644 data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-cats-neuropil.xml
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create mode 100644 scripts/attributes/cilia_attributes.py
diff --git a/data/0.5.1/images/prospr-6dpf-1-whole-AChE-MED.xml b/data/0.5.1/images/prospr-6dpf-1-whole-AChE-MED.xml
new file mode 100644
index 0000000..20a7342
--- /dev/null
+++ b/data/0.5.1/images/prospr-6dpf-1-whole-AChE-MED.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../rawdata/prospr-6dpf-1-whole-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/0.5.1/images/prospr-6dpf-1-whole-ANPRA-MED.xml b/data/0.5.1/images/prospr-6dpf-1-whole-ANPRA-MED.xml
new file mode 100644
index 0000000..0238043
--- /dev/null
+++ b/data/0.5.1/images/prospr-6dpf-1-whole-ANPRA-MED.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../rawdata/prospr-6dpf-1-whole-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/0.5.1/images/prospr-6dpf-1-whole-ANPRB-MED.xml b/data/0.5.1/images/prospr-6dpf-1-whole-ANPRB-MED.xml
new file mode 100644
index 0000000..65280fe
--- /dev/null
+++ b/data/0.5.1/images/prospr-6dpf-1-whole-ANPRB-MED.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../rawdata/prospr-6dpf-1-whole-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>
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+ </ViewRegistration>
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new file mode 100644
index 0000000..0f3187b
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index 0000000..2197237
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index 0000000..a964ec3
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index 0000000..b335505
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index 0000000..9e79660
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new file mode 100644
index 0000000..d19f795
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new file mode 100644
index 0000000..1cdaa78
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new file mode 100644
index 0000000..aad6884
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new file mode 100644
index 0000000..2734a08
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new file mode 100644
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index 0000000..44e306c
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index 0000000..1176bbe
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index 0000000..6c4ac4e
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index 0000000..43bea68
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index 0000000..d0ac410
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index 0000000..da4aa7e
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index 0000000..bf3bd26
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new file mode 100644
index 0000000..7da0200
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index 0000000..a63e103
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index 0000000..e47fac4
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index 0000000..d0d4763
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new file mode 100644
index 0000000..217547c
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new file mode 100644
index 0000000..176894b
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index 0000000..78a230a
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new file mode 100644
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new file mode 100644
index 0000000..e0931f9
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index 0000000..ec4d704
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index 0000000..9a34101
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index 0000000..d911f82
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index 0000000..f08d01c
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index 0000000..1d97324
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index 0000000..d6b17cf
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index 0000000..36f3431
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index 0000000..71584ae
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index 0000000..a25f26e
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index 0000000..67da6f7
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+ <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/0.5.1/images/prospr-6dpf-1-whole-six4-MED.xml b/data/0.5.1/images/prospr-6dpf-1-whole-six4-MED.xml
new file mode 100644
index 0000000..36da934
--- /dev/null
+++ b/data/0.5.1/images/prospr-6dpf-1-whole-six4-MED.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../rawdata/prospr-6dpf-1-whole-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/0.5.1/images/prospr-6dpf-1-whole-tlx-MED.xml b/data/0.5.1/images/prospr-6dpf-1-whole-tlx-MED.xml
new file mode 100644
index 0000000..c46b3f0
--- /dev/null
+++ b/data/0.5.1/images/prospr-6dpf-1-whole-tlx-MED.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../rawdata/prospr-6dpf-1-whole-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/0.5.1/images/prospr-6dpf-1-whole-trk-MED.xml b/data/0.5.1/images/prospr-6dpf-1-whole-trk-MED.xml
new file mode 100644
index 0000000..2897cc4
--- /dev/null
+++ b/data/0.5.1/images/prospr-6dpf-1-whole-trk-MED.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../rawdata/prospr-6dpf-1-whole-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/0.5.1/images/prospr-6dpf-1-whole-uncx-MED.xml b/data/0.5.1/images/prospr-6dpf-1-whole-uncx-MED.xml
new file mode 100644
index 0000000..f466fd7
--- /dev/null
+++ b/data/0.5.1/images/prospr-6dpf-1-whole-uncx-MED.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../rawdata/prospr-6dpf-1-whole-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/data/0.5.1/images/sbem-6dpf-1-whole-mask-inside.xml b/data/0.5.1/images/sbem-6dpf-1-whole-mask-inside.xml
new file mode 100644
index 0000000..9c923a7
--- /dev/null
+++ b/data/0.5.1/images/sbem-6dpf-1-whole-mask-inside.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../rawdata/sbem-6dpf-1-whole-mask-inside.h5</hdf5>
+ </ImageLoader>
+ <ViewSetups>
+ <Attributes name="channel">
+ <Channel>
+ <id>0</id>
+ <name>0</name>
+ </Channel>
+ </Attributes>
+ <ViewSetup>
+ <id>0</id>
+ <name>Setup0</name>
+ <size>860 810 714</size>
+ <voxelSize>
+ <unit>micrometer</unit>
+ <size>0.32 0.32 0.4</size>
+ </voxelSize>
+ <attributes>
+ <channel>0</channel>
+ </attributes>
+ </ViewSetup>
+ </ViewSetups>
+ <Timepoints type="range">
+ <first>0</first>
+ <last>0</last>
+ </Timepoints>
+ </SequenceDescription>
+ <ViewRegistrations>
+ <ViewRegistration setup="0" timepoint="0">
+ <ViewTransform type="affine">
+ <affine>0.32 0.0 0.0 0.0 0.0 0.32 0.0 0.0 0.0 0.0 0.4 0.0</affine>
+ </ViewTransform>
+ </ViewRegistration>
+ </ViewRegistrations>
+</SpimData>
diff --git a/data/0.5.1/images/sbem-6dpf-1-whole-mask-outside.xml b/data/0.5.1/images/sbem-6dpf-1-whole-mask-outside.xml
new file mode 100644
index 0000000..5f3be7f
--- /dev/null
+++ b/data/0.5.1/images/sbem-6dpf-1-whole-mask-outside.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../rawdata/sbem-6dpf-1-whole-mask-outside.h5</hdf5>
+ </ImageLoader>
+ <ViewSetups>
+ <Attributes name="channel">
+ <Channel>
+ <id>0</id>
+ <name>0</name>
+ </Channel>
+ </Attributes>
+ <ViewSetup>
+ <id>0</id>
+ <name>Setup0</name>
+ <size>860 810 714</size>
+ <voxelSize>
+ <unit>micrometer</unit>
+ <size>0.32 0.32 0.4</size>
+ </voxelSize>
+ <attributes>
+ <channel>0</channel>
+ </attributes>
+ </ViewSetup>
+ </ViewSetups>
+ <Timepoints type="range">
+ <first>0</first>
+ <last>0</last>
+ </Timepoints>
+ </SequenceDescription>
+ <ViewRegistrations>
+ <ViewRegistration setup="0" timepoint="0">
+ <ViewTransform type="affine">
+ <affine>0.32 0.0 0.0 0.0 0.0 0.32 0.0 0.0 0.0 0.0 0.4 0.0</affine>
+ </ViewTransform>
+ </ViewRegistration>
+ </ViewRegistrations>
+</SpimData>
diff --git a/data/0.5.1/images/sbem-6dpf-1-whole-mask-resin.xml b/data/0.5.1/images/sbem-6dpf-1-whole-mask-resin.xml
new file mode 100644
index 0000000..f71df8d
--- /dev/null
+++ b/data/0.5.1/images/sbem-6dpf-1-whole-mask-resin.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../rawdata/sbem-6dpf-1-whole-mask-resin.h5</hdf5>
+ </ImageLoader>
+ <ViewSetups>
+ <Attributes name="channel">
+ <Channel>
+ <id>0</id>
+ <name>0</name>
+ </Channel>
+ </Attributes>
+ <ViewSetup>
+ <id>0</id>
+ <name>Setup0</name>
+ <size>860 811 11416</size>
+ <voxelSize>
+ <unit>micrometer</unit>
+ <size>0.32 0.32 0.025</size>
+ </voxelSize>
+ <attributes>
+ <channel>0</channel>
+ </attributes>
+ </ViewSetup>
+ </ViewSetups>
+ <Timepoints type="range">
+ <first>0</first>
+ <last>0</last>
+ </Timepoints>
+ </SequenceDescription>
+ <ViewRegistrations>
+ <ViewRegistration setup="0" timepoint="0">
+ <ViewTransform type="affine">
+ <affine>0.32 0.0 0.0 0.0 0.0 0.32 0.0 0.0 0.0 0.0 0.025 0.0</affine>
+ </ViewTransform>
+ </ViewRegistration>
+ </ViewRegistrations>
+</SpimData>
diff --git a/data/0.5.1/images/sbem-6dpf-1-whole-raw.xml b/data/0.5.1/images/sbem-6dpf-1-whole-raw.xml
new file mode 100644
index 0000000..fcf8dfd
--- /dev/null
+++ b/data/0.5.1/images/sbem-6dpf-1-whole-raw.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../rawdata/sbem-6dpf-1-whole-raw.h5</hdf5>
+ </ImageLoader>
+ <ViewSetups>
+ <Attributes name="channel">
+ <Channel>
+ <id>1</id>
+ <name>1</name>
+ </Channel>
+ </Attributes>
+ <ViewSetup>
+ <id>0</id>
+ <name>channel 1</name>
+ <size>27499 25916 11416</size>
+ <voxelSize>
+ <unit>micrometer</unit>
+ <size>0.01 0.01 0.025</size>
+ </voxelSize>
+ <attributes>
+ <channel>1</channel>
+ </attributes>
+ </ViewSetup>
+ </ViewSetups>
+ <Timepoints type="range">
+ <first>0</first>
+ <last>0</last>
+ </Timepoints>
+ </SequenceDescription>
+ <ViewRegistrations>
+ <ViewRegistration setup="0" timepoint="0">
+ <ViewTransform type="affine">
+ <affine>0.01 0.0 0.0 0.0 0.0 0.01 0.0 0.0 0.0 0.0 0.025 0.0</affine>
+ </ViewTransform>
+ </ViewRegistration>
+ </ViewRegistrations>
+</SpimData>
diff --git a/data/0.5.1/misc/bdv_server.txt b/data/0.5.1/misc/bdv_server.txt
new file mode 100644
index 0000000..381e6a4
--- /dev/null
+++ b/data/0.5.1/misc/bdv_server.txt
@@ -0,0 +1,221 @@
+sbem-6dpf-1-whole-raw ../images/sbem-6dpf-1-whole-raw.xml
+prospr-6dpf-1-whole-AChE-MED ../images/prospr-6dpf-1-whole-AChE-MED.xml
+prospr-6dpf-1-whole-ANPRA-MED ../images/prospr-6dpf-1-whole-ANPRA-MED.xml
+prospr-6dpf-1-whole-ANPRB-MED ../images/prospr-6dpf-1-whole-ANPRB-MED.xml
+prospr-6dpf-1-whole-AP2-MED ../images/prospr-6dpf-1-whole-AP2-MED.xml
+prospr-6dpf-1-whole-ASCb-MED ../images/prospr-6dpf-1-whole-ASCb-MED.xml
+prospr-6dpf-1-whole-AcTub-MED ../images/prospr-6dpf-1-whole-AcTub-MED.xml
+prospr-6dpf-1-whole-AllCR1-MED ../images/prospr-6dpf-1-whole-AllCR1-MED.xml
+prospr-6dpf-1-whole-AllCR2-MED ../images/prospr-6dpf-1-whole-AllCR2-MED.xml
+prospr-6dpf-1-whole-Arx-MED ../images/prospr-6dpf-1-whole-Arx-MED.xml
+prospr-6dpf-1-whole-Ash-MED ../images/prospr-6dpf-1-whole-Ash-MED.xml
+prospr-6dpf-1-whole-BAIAP-MED ../images/prospr-6dpf-1-whole-BAIAP-MED.xml
+prospr-6dpf-1-whole-BarH1-MED ../images/prospr-6dpf-1-whole-BarH1-MED.xml
+prospr-6dpf-1-whole-Beta3-MED ../images/prospr-6dpf-1-whole-Beta3-MED.xml
+prospr-6dpf-1-whole-Bmpr1-MED ../images/prospr-6dpf-1-whole-Bmpr1-MED.xml
+prospr-6dpf-1-whole-Brn3a-MED ../images/prospr-6dpf-1-whole-Brn3a-MED.xml
+prospr-6dpf-1-whole-COE-MED ../images/prospr-6dpf-1-whole-COE-MED.xml
+prospr-6dpf-1-whole-Cal2-MED ../images/prospr-6dpf-1-whole-Cal2-MED.xml
+prospr-6dpf-1-whole-Calmodulin-MED ../images/prospr-6dpf-1-whole-Calmodulin-MED.xml
+prospr-6dpf-1-whole-ChAT-MED ../images/prospr-6dpf-1-whole-ChAT-MED.xml
+prospr-6dpf-1-whole-Chx10-MED ../images/prospr-6dpf-1-whole-Chx10-MED.xml
+prospr-6dpf-1-whole-Dach-MED ../images/prospr-6dpf-1-whole-Dach-MED.xml
+prospr-6dpf-1-whole-DbhLike-MED ../images/prospr-6dpf-1-whole-DbhLike-MED.xml
+prospr-6dpf-1-whole-DopaRD2-MED ../images/prospr-6dpf-1-whole-DopaRD2-MED.xml
+prospr-6dpf-1-whole-ENR1-MED ../images/prospr-6dpf-1-whole-ENR1-MED.xml
+prospr-6dpf-1-whole-ENR10-MED ../images/prospr-6dpf-1-whole-ENR10-MED.xml
+prospr-6dpf-1-whole-ENR12-MED ../images/prospr-6dpf-1-whole-ENR12-MED.xml
+prospr-6dpf-1-whole-ENR13-MED ../images/prospr-6dpf-1-whole-ENR13-MED.xml
+prospr-6dpf-1-whole-ENR16-MED ../images/prospr-6dpf-1-whole-ENR16-MED.xml
+prospr-6dpf-1-whole-ENR19-MED ../images/prospr-6dpf-1-whole-ENR19-MED.xml
+prospr-6dpf-1-whole-ENR2-MED ../images/prospr-6dpf-1-whole-ENR2-MED.xml
+prospr-6dpf-1-whole-ENR20-MED ../images/prospr-6dpf-1-whole-ENR20-MED.xml
+prospr-6dpf-1-whole-ENR22-MED ../images/prospr-6dpf-1-whole-ENR22-MED.xml
+prospr-6dpf-1-whole-ENR25-MED ../images/prospr-6dpf-1-whole-ENR25-MED.xml
+prospr-6dpf-1-whole-ENR29-MED ../images/prospr-6dpf-1-whole-ENR29-MED.xml
+prospr-6dpf-1-whole-ENR3-MED ../images/prospr-6dpf-1-whole-ENR3-MED.xml
+prospr-6dpf-1-whole-ENR30-MED ../images/prospr-6dpf-1-whole-ENR30-MED.xml
+prospr-6dpf-1-whole-ENR31-MED ../images/prospr-6dpf-1-whole-ENR31-MED.xml
+prospr-6dpf-1-whole-ENR32-MED ../images/prospr-6dpf-1-whole-ENR32-MED.xml
+prospr-6dpf-1-whole-ENR34-MED ../images/prospr-6dpf-1-whole-ENR34-MED.xml
+prospr-6dpf-1-whole-ENR39-MED ../images/prospr-6dpf-1-whole-ENR39-MED.xml
+prospr-6dpf-1-whole-ENR4-MED ../images/prospr-6dpf-1-whole-ENR4-MED.xml
+prospr-6dpf-1-whole-ENR46-MED ../images/prospr-6dpf-1-whole-ENR46-MED.xml
+prospr-6dpf-1-whole-ENR6-MED ../images/prospr-6dpf-1-whole-ENR6-MED.xml
+prospr-6dpf-1-whole-ENR54-MED ../images/prospr-6dpf-1-whole-ENR54-MED.xml
+prospr-6dpf-1-whole-ENR57-MED ../images/prospr-6dpf-1-whole-ENR57-MED.xml
+prospr-6dpf-1-whole-ENR62-MED ../images/prospr-6dpf-1-whole-ENR62-MED.xml
+prospr-6dpf-1-whole-ENR64-MED ../images/prospr-6dpf-1-whole-ENR64-MED.xml
+prospr-6dpf-1-whole-ENR69-MED ../images/prospr-6dpf-1-whole-ENR69-MED.xml
+prospr-6dpf-1-whole-ENR71-MED ../images/prospr-6dpf-1-whole-ENR71-MED.xml
+prospr-6dpf-1-whole-ENR8-MED ../images/prospr-6dpf-1-whole-ENR8-MED.xml
+prospr-6dpf-1-whole-ENR9-MED ../images/prospr-6dpf-1-whole-ENR9-MED.xml
+prospr-6dpf-1-whole-ElaV-MED ../images/prospr-6dpf-1-whole-ElaV-MED.xml
+prospr-6dpf-1-whole-FOR-MED ../images/prospr-6dpf-1-whole-FOR-MED.xml
+prospr-6dpf-1-whole-FVRI-MED ../images/prospr-6dpf-1-whole-FVRI-MED.xml
+prospr-6dpf-1-whole-FoxD3-MED ../images/prospr-6dpf-1-whole-FoxD3-MED.xml
+prospr-6dpf-1-whole-FoxN4-MED ../images/prospr-6dpf-1-whole-FoxN4-MED.xml
+prospr-6dpf-1-whole-GAD-MED ../images/prospr-6dpf-1-whole-GAD-MED.xml
+prospr-6dpf-1-whole-GCB-MED ../images/prospr-6dpf-1-whole-GCB-MED.xml
+prospr-6dpf-1-whole-GCD-MED ../images/prospr-6dpf-1-whole-GCD-MED.xml
+prospr-6dpf-1-whole-GPCR2-MED ../images/prospr-6dpf-1-whole-GPCR2-MED.xml
+prospr-6dpf-1-whole-GPCR203-MED ../images/prospr-6dpf-1-whole-GPCR203-MED.xml
+prospr-6dpf-1-whole-GPCR209-MED ../images/prospr-6dpf-1-whole-GPCR209-MED.xml
+prospr-6dpf-1-whole-GPCR210-MED ../images/prospr-6dpf-1-whole-GPCR210-MED.xml
+prospr-6dpf-1-whole-GPCR32-MED ../images/prospr-6dpf-1-whole-GPCR32-MED.xml
+prospr-6dpf-1-whole-GPPCR21-MED ../images/prospr-6dpf-1-whole-GPPCR21-MED.xml
+prospr-6dpf-1-whole-Gata123-MED ../images/prospr-6dpf-1-whole-Gata123-MED.xml
+prospr-6dpf-1-whole-Glt1-MED ../images/prospr-6dpf-1-whole-Glt1-MED.xml
+prospr-6dpf-1-whole-GlyT-MED ../images/prospr-6dpf-1-whole-GlyT-MED.xml
+prospr-6dpf-1-whole-GnRH-MED ../images/prospr-6dpf-1-whole-GnRH-MED.xml
+prospr-6dpf-1-whole-GnrhR-MED ../images/prospr-6dpf-1-whole-GnrhR-MED.xml
+prospr-6dpf-1-whole-Grm7-MED ../images/prospr-6dpf-1-whole-Grm7-MED.xml
+prospr-6dpf-1-whole-Gucy-MED ../images/prospr-6dpf-1-whole-Gucy-MED.xml
+prospr-6dpf-1-whole-HCN1-MED ../images/prospr-6dpf-1-whole-HCN1-MED.xml
+prospr-6dpf-1-whole-HNF6-MED ../images/prospr-6dpf-1-whole-HNF6-MED.xml
+prospr-6dpf-1-whole-Hand-MED ../images/prospr-6dpf-1-whole-Hand-MED.xml
+prospr-6dpf-1-whole-Hb9-MED ../images/prospr-6dpf-1-whole-Hb9-MED.xml
+prospr-6dpf-1-whole-Hox5-MED ../images/prospr-6dpf-1-whole-Hox5-MED.xml
+prospr-6dpf-1-whole-Hox7-MED ../images/prospr-6dpf-1-whole-Hox7-MED.xml
+prospr-6dpf-1-whole-Hr38-MED ../images/prospr-6dpf-1-whole-Hr38-MED.xml
+prospr-6dpf-1-whole-Isl-MED ../images/prospr-6dpf-1-whole-Isl-MED.xml
+prospr-6dpf-1-whole-Kv33b-MED ../images/prospr-6dpf-1-whole-Kv33b-MED.xml
+prospr-6dpf-1-whole-Kv33e-MED ../images/prospr-6dpf-1-whole-Kv33e-MED.xml
+prospr-6dpf-1-whole-Lhx15-MED ../images/prospr-6dpf-1-whole-Lhx15-MED.xml
+prospr-6dpf-1-whole-Lhx2-MED ../images/prospr-6dpf-1-whole-Lhx2-MED.xml
+prospr-6dpf-1-whole-Lhx3-MED ../images/prospr-6dpf-1-whole-Lhx3-MED.xml
+prospr-6dpf-1-whole-Lmo4-MED ../images/prospr-6dpf-1-whole-Lmo4-MED.xml
+prospr-6dpf-1-whole-Lmx1-MED ../images/prospr-6dpf-1-whole-Lmx1-MED.xml
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+prospr-6dpf-1-whole-NPR1a-MED ../images/prospr-6dpf-1-whole-NPR1a-MED.xml
+prospr-6dpf-1-whole-Netrin-MED ../images/prospr-6dpf-1-whole-Netrin-MED.xml
+prospr-6dpf-1-whole-NeuroD-MED ../images/prospr-6dpf-1-whole-NeuroD-MED.xml
+prospr-6dpf-1-whole-Ngb-MED ../images/prospr-6dpf-1-whole-Ngb-MED.xml
+prospr-6dpf-1-whole-Olig-MED ../images/prospr-6dpf-1-whole-Olig-MED.xml
+prospr-6dpf-1-whole-P56-MED ../images/prospr-6dpf-1-whole-P56-MED.xml
+prospr-6dpf-1-whole-PCDH15-MED ../images/prospr-6dpf-1-whole-PCDH15-MED.xml
+prospr-6dpf-1-whole-PDF-MED ../images/prospr-6dpf-1-whole-PDF-MED.xml
+prospr-6dpf-1-whole-PLCg-MED ../images/prospr-6dpf-1-whole-PLCg-MED.xml
+prospr-6dpf-1-whole-Pax258-MED ../images/prospr-6dpf-1-whole-Pax258-MED.xml
+prospr-6dpf-1-whole-Pax6-MED ../images/prospr-6dpf-1-whole-Pax6-MED.xml
+prospr-6dpf-1-whole-Pde9-MED ../images/prospr-6dpf-1-whole-Pde9-MED.xml
+prospr-6dpf-1-whole-Pea3-MED ../images/prospr-6dpf-1-whole-Pea3-MED.xml
+prospr-6dpf-1-whole-Phc2-MED ../images/prospr-6dpf-1-whole-Phc2-MED.xml
+prospr-6dpf-1-whole-Phox2b-MED ../images/prospr-6dpf-1-whole-Phox2b-MED.xml
+prospr-6dpf-1-whole-Pikachu-MED ../images/prospr-6dpf-1-whole-Pikachu-MED.xml
+prospr-6dpf-1-whole-PitxB-MED ../images/prospr-6dpf-1-whole-PitxB-MED.xml
+prospr-6dpf-1-whole-Prdm8-MED ../images/prospr-6dpf-1-whole-Prdm8-MED.xml
+prospr-6dpf-1-whole-Prox-MED ../images/prospr-6dpf-1-whole-Prox-MED.xml
+prospr-6dpf-1-whole-Ptf1-MED ../images/prospr-6dpf-1-whole-Ptf1-MED.xml
+prospr-6dpf-1-whole-Pty2-MED ../images/prospr-6dpf-1-whole-Pty2-MED.xml
+prospr-6dpf-1-whole-RIMS-MED ../images/prospr-6dpf-1-whole-RIMS-MED.xml
+prospr-6dpf-1-whole-Rab3-MED ../images/prospr-6dpf-1-whole-Rab3-MED.xml
+prospr-6dpf-1-whole-Robo-MED ../images/prospr-6dpf-1-whole-Robo-MED.xml
+prospr-6dpf-1-whole-Scn8aa-MED ../images/prospr-6dpf-1-whole-Scn8aa-MED.xml
+prospr-6dpf-1-whole-Sema2-MED ../images/prospr-6dpf-1-whole-Sema2-MED.xml
+prospr-6dpf-1-whole-Sim1-MED ../images/prospr-6dpf-1-whole-Sim1-MED.xml
+prospr-6dpf-1-whole-Slit-MED ../images/prospr-6dpf-1-whole-Slit-MED.xml
+prospr-6dpf-1-whole-Sox2-MED ../images/prospr-6dpf-1-whole-Sox2-MED.xml
+prospr-6dpf-1-whole-Sox4-MED ../images/prospr-6dpf-1-whole-Sox4-MED.xml
+prospr-6dpf-1-whole-SoxB12-MED ../images/prospr-6dpf-1-whole-SoxB12-MED.xml
+prospr-6dpf-1-whole-SoxB2-MED ../images/prospr-6dpf-1-whole-SoxB2-MED.xml
+prospr-6dpf-1-whole-Sp8-MED ../images/prospr-6dpf-1-whole-Sp8-MED.xml
+prospr-6dpf-1-whole-Syt-MED ../images/prospr-6dpf-1-whole-Syt-MED.xml
+prospr-6dpf-1-whole-Syt12-MED ../images/prospr-6dpf-1-whole-Syt12-MED.xml
+prospr-6dpf-1-whole-Syt7-MED ../images/prospr-6dpf-1-whole-Syt7-MED.xml
+prospr-6dpf-1-whole-Syta-MED ../images/prospr-6dpf-1-whole-Syta-MED.xml
+prospr-6dpf-1-whole-TH-MED ../images/prospr-6dpf-1-whole-TH-MED.xml
+prospr-6dpf-1-whole-TIMP-MED ../images/prospr-6dpf-1-whole-TIMP-MED.xml
+prospr-6dpf-1-whole-TRPV4-MED ../images/prospr-6dpf-1-whole-TRPV4-MED.xml
+prospr-6dpf-1-whole-TRPV5-MED ../images/prospr-6dpf-1-whole-TRPV5-MED.xml
+prospr-6dpf-1-whole-Tal-MED ../images/prospr-6dpf-1-whole-Tal-MED.xml
+prospr-6dpf-1-whole-Tbh-MED ../images/prospr-6dpf-1-whole-Tbh-MED.xml
+prospr-6dpf-1-whole-Tbx20-MED ../images/prospr-6dpf-1-whole-Tbx20-MED.xml
+prospr-6dpf-1-whole-TrpH-MED ../images/prospr-6dpf-1-whole-TrpH-MED.xml
+prospr-6dpf-1-whole-TrpV-MED ../images/prospr-6dpf-1-whole-TrpV-MED.xml
+prospr-6dpf-1-whole-Twist-MED ../images/prospr-6dpf-1-whole-Twist-MED.xml
+prospr-6dpf-1-whole-UNCS-MED ../images/prospr-6dpf-1-whole-UNCS-MED.xml
+prospr-6dpf-1-whole-VAChT-MED ../images/prospr-6dpf-1-whole-VAChT-MED.xml
+prospr-6dpf-1-whole-VAT1L-MED ../images/prospr-6dpf-1-whole-VAT1L-MED.xml
+prospr-6dpf-1-whole-VGluT-MED ../images/prospr-6dpf-1-whole-VGluT-MED.xml
+prospr-6dpf-1-whole-VegfR-MED ../images/prospr-6dpf-1-whole-VegfR-MED.xml
+prospr-6dpf-1-whole-Wnt16-MED ../images/prospr-6dpf-1-whole-Wnt16-MED.xml
+prospr-6dpf-1-whole-Wnt5-MED ../images/prospr-6dpf-1-whole-Wnt5-MED.xml
+prospr-6dpf-1-whole-ascI-MED ../images/prospr-6dpf-1-whole-ascI-MED.xml
+prospr-6dpf-1-whole-ascII-MED ../images/prospr-6dpf-1-whole-ascII-MED.xml
+prospr-6dpf-1-whole-asicalpha-MED ../images/prospr-6dpf-1-whole-asicalpha-MED.xml
+prospr-6dpf-1-whole-bsx-MED ../images/prospr-6dpf-1-whole-bsx-MED.xml
+prospr-6dpf-1-whole-catL-MED ../images/prospr-6dpf-1-whole-catL-MED.xml
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+prospr-6dpf-1-whole-delta-MED ../images/prospr-6dpf-1-whole-delta-MED.xml
+prospr-6dpf-1-whole-dlx-MED ../images/prospr-6dpf-1-whole-dlx-MED.xml
+prospr-6dpf-1-whole-edu3to4at6dpf-MED ../images/prospr-6dpf-1-whole-edu3to4at6dpf-MED.xml
+prospr-6dpf-1-whole-edu4to5at6dpf-MED ../images/prospr-6dpf-1-whole-edu4to5at6dpf-MED.xml
+prospr-6dpf-1-whole-edu5to6at6dpf-MED ../images/prospr-6dpf-1-whole-edu5to6at6dpf-MED.xml
+prospr-6dpf-1-whole-eve-MED ../images/prospr-6dpf-1-whole-eve-MED.xml
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+prospr-6dpf-1-whole-six4-MED ../images/prospr-6dpf-1-whole-six4-MED.xml
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+prospr-6dpf-1-whole-segmented-Pygidium ../images/prospr-6dpf-1-whole-segmented-Pygidium.xml
+prospr-6dpf-1-whole-segmented-RestOfAnimal ../images/prospr-6dpf-1-whole-segmented-RestOfAnimal.xml
+prospr-6dpf-1-whole-segmented-Stomodeum ../images/prospr-6dpf-1-whole-segmented-Stomodeum.xml
+prospr-6dpf-1-whole-segmented-VNC ../images/prospr-6dpf-1-whole-segmented-VNC.xml
+prospr-6dpf-1-whole-six12-MED ../images/prospr-6dpf-1-whole-six12-MED.xml
+prospr-6dpf-1-whole-ref-SPM ../images/prospr-6dpf-1-whole-ref-SPM.xml
+sbem-6dpf-1-whole-mask-resin ../images/sbem-6dpf-1-whole-mask-resin.xml
+sbem-6dpf-1-whole-mask-inside ../images/sbem-6dpf-1-whole-mask-inside.xml
+sbem-6dpf-1-whole-mask-outside ../images/sbem-6dpf-1-whole-mask-outside.xml
+sbem-6dpf-1-whole-segmented-chromatin-labels ../segmentations/sbem-6dpf-1-whole-segmented-chromatin-labels.xml
+sbem-6dpf-1-whole-segmented-tissue-labels ../segmentations/sbem-6dpf-1-whole-segmented-tissue-labels.xml
+sbem-6dpf-1-whole-segmented-muscle ../segmentations/sbem-6dpf-1-whole-segmented-muscle.xml
+sbem-6dpf-1-whole-segmented-cells-labels ../segmentations/sbem-6dpf-1-whole-segmented-cells-labels.xml
+sbem-6dpf-1-whole-segmented-nuclei-labels ../segmentations/sbem-6dpf-1-whole-segmented-nuclei-labels.xml
+sbem-6dpf-1-whole-segmented-cilia-labels ../segmentations/sbem-6dpf-1-whole-segmented-cilia-labels.xml
+sbem-6dpf-1-whole-segmented-ariande-neuropil ../segmentations/sbem-6dpf-1-whole-segmented-ariande-neuropil.xml
+sbem-6dpf-1-whole-segmented-cats-neuropil ../segmentations/sbem-6dpf-1-whole-segmented-cats-neuropil.xml
diff --git a/data/0.5.1/misc/bookmarks.json b/data/0.5.1/misc/bookmarks.json
new file mode 100644
index 0000000..95f90ac
--- /dev/null
+++ b/data/0.5.1/misc/bookmarks.json
@@ -0,0 +1,6 @@
+{"Nephridia1": {"Position": [96.60291585539845,146.7972323927267,185.4679511451342]},
+ "Nephridia1-end-of-cilia": {
+ "Position": [70.98852643983105,121.02217692079869,218.4184352478732],
+ "View": [174.04825917939706, 10.36809012953386, -5.569983118834367, -11165.611289377557, -11.73197046208067, 159.42513426035973, -69.83771161342541, -2366.2978168440077, 0.93961372654079, 70.0531783817763, 159.75915577178273, -43439.03476204738]},
+ "Left eye": {"Position": [70.98852643983105,121.02217692079869,218.4184352478732]}
+}
diff --git a/data/0.5.1/misc/cilia_id_mapping.csv b/data/0.5.1/misc/cilia_id_mapping.csv
new file mode 100644
index 0000000..fa56ec8
--- /dev/null
+++ b/data/0.5.1/misc/cilia_id_mapping.csv
@@ -0,0 +1,125 @@
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diff --git a/data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-cells-labels.json b/data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-cells-labels.json
new file mode 120000
index 0000000..3c5c7e2
--- /dev/null
+++ b/data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-cells-labels.json
@@ -0,0 +1 @@
+../../0.5.0/misc/new_id_lut_sbem-6dpf-1-whole-segmented-cells-labels.json
\ No newline at end of file
diff --git a/data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-cilia-labels.json b/data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-cilia-labels.json
new file mode 100644
index 0000000..06744bc
--- /dev/null
+++ b/data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-cilia-labels.json
@@ -0,0 +1 @@
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diff --git a/data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-nuclei-labels.json b/data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-nuclei-labels.json
new file mode 120000
index 0000000..13e8739
--- /dev/null
+++ b/data/0.5.1/misc/new_id_lut_sbem-6dpf-1-whole-segmented-nuclei-labels.json
@@ -0,0 +1 @@
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\ No newline at end of file
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new file mode 100644
index 0000000..cedbbbc
--- /dev/null
+++ b/data/0.5.1/misc/prospr-6dpf-1-whole_meds_all_genes.xml
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+<SpimData version="0.2">
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diff --git a/data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-ariande-neuropil.xml b/data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-ariande-neuropil.xml
new file mode 100644
index 0000000..2b06347
--- /dev/null
+++ b/data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-ariande-neuropil.xml
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new file mode 100644
index 0000000..4ea187a
--- /dev/null
+++ b/data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-cats-neuropil.xml
@@ -0,0 +1,39 @@
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+ <voxelSize>
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+ <size>0.5 0.5 0.5</size>
+ </voxelSize>
+ <attributes>
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+ </ViewSetup>
+ <Attributes name="channel">
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+ </ViewRegistration>
+ </ViewRegistrations>
+</SpimData>
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new file mode 100644
index 0000000..2d6e272
--- /dev/null
+++ b/data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-cells-labels.xml
@@ -0,0 +1,39 @@
+<SpimData version="0.2">
+ <BasePath type="relative">.</BasePath>
+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
+ <hdf5 type="relative">../../0.3.1/segmentations/sbem-6dpf-1-whole-segmented-cells-labels.h5</hdf5>
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+ <ViewSetups>
+ <Attributes name="channel">
+ <Channel>
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diff --git a/data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-chromatin-labels.xml b/data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-chromatin-labels.xml
new file mode 100644
index 0000000..25dd2b4
--- /dev/null
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@@ -0,0 +1,39 @@
+<SpimData version="0.2">
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+ <SequenceDescription>
+ <ImageLoader format="bdv.hdf5">
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new file mode 100644
index 0000000..f06bacd
--- /dev/null
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@@ -0,0 +1,39 @@
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+ <size>27499 25916 11416</size>
+ <voxelSize>
+ <unit>micrometer</unit>
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diff --git a/data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-muscle.xml b/data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-muscle.xml
new file mode 100644
index 0000000..26ba713
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new file mode 100644
index 0000000..f818c38
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new file mode 100644
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new file mode 100644
index 0000000..e3442cd
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diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/cells_to_nuclei.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/cells_to_nuclei.csv
new file mode 120000
index 0000000..558c6aa
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/cells_to_nuclei.csv
@@ -0,0 +1 @@
+../../../0.5.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/cells_to_nuclei.csv
\ No newline at end of file
diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/default.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/default.csv
new file mode 120000
index 0000000..477a6e2
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/default.csv
@@ -0,0 +1 @@
+../../../0.5.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/default.csv
\ No newline at end of file
diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/genes.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/genes.csv
new file mode 120000
index 0000000..0d63714
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/genes.csv
@@ -0,0 +1 @@
+../../../0.5.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/genes.csv
\ No newline at end of file
diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/morphology.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/morphology.csv
new file mode 120000
index 0000000..56717d9
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/morphology.csv
@@ -0,0 +1 @@
+../../../0.5.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/morphology.csv
\ No newline at end of file
diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/regions.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/regions.csv
new file mode 120000
index 0000000..f0ba8d7
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cells-labels/regions.csv
@@ -0,0 +1 @@
+../../../0.5.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/regions.csv
\ No newline at end of file
diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-chromatin-labels/default.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-chromatin-labels/default.csv
new file mode 120000
index 0000000..10b9849
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-chromatin-labels/default.csv
@@ -0,0 +1 @@
+../../../0.5.0/tables/sbem-6dpf-1-whole-segmented-chromatin-labels/default.csv
\ No newline at end of file
diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/cilia.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/cilia.csv
new file mode 100644
index 0000000..891ed3a
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/cilia.csv
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diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/default.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/default.csv
new file mode 100644
index 0000000..4fd55f9
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/default.csv
@@ -0,0 +1,533 @@
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diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/default.csv.bkp b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/default.csv.bkp
new file mode 100644
index 0000000..ec8eb20
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/default.csv.bkp
@@ -0,0 +1,533 @@
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+518.0 74.40083312988281 121.93702697753906 216.90879821777344 73.85000000000001 121.68 216.60000000000002 74.9 122.2 217.25 29577.0
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+520.0 79.33375549316406 125.0643539428711 217.31484985351562 79.27 124.62 217.0 79.35000000000001 125.43 217.47500000000002 1109.0
+521.0 79.15748596191406 122.79068756103516 218.34597778320312 79.04 122.64 218.22500000000002 79.29 122.87 218.47500000000002 3046.0
+522.0 70.46351623535156 120.378173828125 219.8382110595703 70.28 120.19 219.55 70.78 120.5 219.95000000000002 2358.0
+523.0 188.58941650390625 92.37326049804688 180.37852478027344 188.36 91.65 180.3 188.88 92.77 180.47500000000002 10064.0
+524.0 188.79820251464844 92.1431884765625 180.35641479492188 188.66 92.01 180.35000000000002 188.94 92.31 180.375 1069.0
+525.0 138.6947784423828 82.70723724365234 184.2708740234375 134.92000000000002 73.24 184.10000000000002 139.12 83.26 196.72500000000002 771308.0
+526.0 175.4880828857422 83.1871566772461 178.2750701904297 172.6 83.01 178.675 182.52 85.72 181.425 341426.0
+527.0 176.76785278320312 84.46696472167969 178.2750701904297 176.28 84.23 178.65 186.3 89.51 180.70000000000002 419338.0
+528.0 177.8876495361328 84.46696472167969 178.2750701904297 177.29 84.43 178.75 187.74 89.7 181.5 403406.0
+529.0 95.82257843017578 143.1779022216797 187.4686279296875 87.34 135.85 187.55 96.17 143.59 199.375 784160.0
+530.0 87.50408935546875 136.4589385986328 199.46023559570312 82.29 127.26 199.70000000000002 87.8 136.9 210.525 687136.0
+531.0 84.6246109008789 128.94009399414062 207.05491638183594 76.03 122.88 207.10000000000002 85.09 129.4 215.65 639385.0
diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/default.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/default.csv
new file mode 120000
index 0000000..e2d23e6
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/default.csv
@@ -0,0 +1 @@
+../../../0.5.0/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/default.csv
\ No newline at end of file
diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/morphology.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/morphology.csv
new file mode 120000
index 0000000..2d6b85c
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/morphology.csv
@@ -0,0 +1 @@
+../../../0.5.0/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/morphology.csv
\ No newline at end of file
diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-tissue-labels/default.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-tissue-labels/default.csv
new file mode 120000
index 0000000..786bd1c
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-segmented-tissue-labels/default.csv
@@ -0,0 +1 @@
+../../../0.5.0/tables/sbem-6dpf-1-whole-segmented-tissue-labels/default.csv
\ No newline at end of file
diff --git a/data/0.5.1/tables/sbem-6dpf-1-whole-traces-labels/default.csv b/data/0.5.1/tables/sbem-6dpf-1-whole-traces-labels/default.csv
new file mode 120000
index 0000000..bc7c761
--- /dev/null
+++ b/data/0.5.1/tables/sbem-6dpf-1-whole-traces-labels/default.csv
@@ -0,0 +1 @@
+../../../0.5.0/tables/sbem-6dpf-1-whole-traces-labels/default.csv
\ No newline at end of file
diff --git a/data/versions.json b/data/versions.json
index 0ccc70c..d813384 100644
--- a/data/versions.json
+++ b/data/versions.json
@@ -1 +1 @@
-["0.0.0", "0.0.1", "0.1.0", "0.1.1", "0.2.0", "0.2.1", "0.3.0", "0.3.1", "0.4.0", "0.5.0"]
\ No newline at end of file
+["0.0.0", "0.0.1", "0.1.0", "0.1.1", "0.2.0", "0.2.1", "0.3.0", "0.3.1", "0.4.0", "0.5.0", "0.5.1", "0.5.1"]
\ No newline at end of file
diff --git a/scripts/attributes/cilia_attributes.py b/scripts/attributes/cilia_attributes.py
new file mode 100644
index 0000000..5971684
--- /dev/null
+++ b/scripts/attributes/cilia_attributes.py
@@ -0,0 +1,70 @@
+from concurrent import futures
+import numpy as np
+import h5py
+import pandas as pd
+
+
+def get_mapped_cell_ids(cilia_ids, manual_mapping_table_path):
+ mapping_table = pd.read_csv(manual_mapping_table_path, sep='\t')
+
+ cell_ids = np.zeros_like(cilia_ids)
+ for row in mapping_table.itertuples(index=False):
+ cilia_id = int(row.cilia_id)
+ cell_id = int(row.cell_id)
+ cell_ids[cilia_id] = cell_id
+
+ return cell_ids
+
+
+# more atttributes? curvature?
+def measure_cilia_attributes(seg_path, seg_key, base_table, resolution):
+ n_features = 2
+ attributes = np.zeros((len(base_table), n_features), dtype='float32')
+ names = ['length', 'diameter']
+
+ # ids = base_table['cilia_ids'].values.astype('uiint64')
+
+ # TODO
+ # with h5py.File(seg_path, 'r') as f:
+ # ds = f[seg_key]
+
+ # def compute_attributes(cid):
+ # # get the row for this cilia id
+ # row = base_table[cid]
+
+ # # compute the bounding box
+
+ # # load segmentation from the bounding box and get foreground
+
+ # # compute len in microns (via shortest path) and diameter (via mean boundary distance transform)
+
+ # n_threads = 8
+ # with futures.ThreadPoolExecutor(n_threads) as tp:
+ # tasks = [tp.submit(compute_attributes(cid)) for cid in ids[1:]]
+ # [t.result() for t in tasks]
+
+ return attributes, names
+
+
+# TODO wrap this into a luigi task so we don't recompute it every time
+def cilia_attributes(seg_path, seg_key,
+ base_table_path, manual_mapping_table_path, table_out_path,
+ resolution, tmp_folder, target, max_jobs):
+
+ # read the base table
+ base_table = pd.read_csv(base_table_path, sep='\t')
+ cilia_ids = base_table['label_id'].values.astype('uint64')
+
+ # add the manually mapped cell ids
+ cell_ids = get_mapped_cell_ids(cilia_ids, manual_mapping_table_path)
+ assert len(cell_ids) == len(cilia_ids)
+
+ # measure cilia specific attributes: length, diameter, ? (could try curvature)
+ attributes, names = measure_cilia_attributes(seg_path, seg_key, base_table, resolution)
+ assert len(attributes) == len(cilia_ids)
+ assert attributes.shape[1] == len(names)
+
+ table = np.concatenate([cilia_ids[:, None], cell_ids[:, None], attributes], axis=1)
+ col_names = ['label_id', 'cell_id'] + names
+ table = pd.DataFrame(table, columns=col_names)
+ table.to_csv(table_out_path, index=False, sep='\t')
diff --git a/scripts/attributes/master.py b/scripts/attributes/master.py
index d6be5c7..45ac9d7 100644
--- a/scripts/attributes/master.py
+++ b/scripts/attributes/master.py
@@ -6,6 +6,7 @@ from .cell_nucleus_mapping import map_cells_to_nuclei
from .genes import write_genes_table
from .morphology import write_morphology_cells, write_morphology_nuclei
from .region_attributes import region_attributes
+from .cilia_attributes import cilia_attributes
from ..files.xml_utils import get_h5_path_from_xml
@@ -108,5 +109,16 @@ def make_cilia_tables(folder, name, tmp_folder, resolution,
base_attributes(seg_path, seg_key, base_out, resolution,
tmp_folder, target=target, max_jobs=max_jobs,
correct_anchors=True)
- # TODO additional tables:
- # ???
+
+ # TODO need to implement functionality to automatically map the cell ids
+ # between versions of the segmentation
+ manual_mapping_table = os.path.join(folder, 'misc', 'cilia_id_mapping.csv')
+ assert os.path.exists(manual_mapping_table)
+
+ # compute cilia specific attributes at lower resolution ?
+
+ # add cilia specific attributes (length, diameter) and manual cell mapping done by rachel
+ cilia_out = os.path.join(table_folder, 'cilia.csv')
+ cilia_attributes(seg_path, seg_key,
+ base_out, manual_mapping_table, cilia_out,
+ resolution, tmp_folder, target=target, max_jobs=max_jobs)
--
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