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Forked from Christian Tischer / platy-browser-data
241 commits behind the upstream repository.
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Update bdv server script
Constantin Pape authored
85c5fc38
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Name Last commit Last update
data
scripts
test/attributes
.gitignore
README.md
environment.yaml
extract_from_platybrowser.py
legacy_export.py
make_data_sources.py
make_initial_version.py
swap_links.py
update_platy_browser.py
README.md

platy-browser-data

Data and data-generation for the platybrowser.

Data storage

Image data (only links for the image volumes) and derived data for all versions are stored in the folder data. We follow a versioning scheme inspired by semantic versioning, hence all version numbers are given as MAJOR.MINOR.PATCH.

  • PATCH is increased if the derived data is update, e.g. due to corrections in some segmentation or new attributes in some table. This is usually triggered automatically (see section below).
  • MINOR is increased if new derived data is added, e.g. a new segmentation for some structure or a new attribute table. This needs to be done manually.
  • MAJOR is increased if new image / raw data is added, e.g. a new animal registered to the atlas or new genes. This needs to be done manually.

For a given version X.Y.Z, the data is stored in the directory /data/X.Y.Z/ with subfolders:

  • images: Raw image or gene expression data. Contains bigdata-viewer xml files with absolute links to h5 files on the embl server.
  • misc: Miscellanous data.
  • segmentations: Segmentation volumes derived from the image data. Only xml files.
  • tables: CSV tables with attributes derived from image data and segmentations.

File naming

Xml / hdf5 filenames must adhere to the following naming scheme, in order to clearly identify the origin of the data: the names must be prefixed by the header MODALITY-STAGE-ID-REGION, where

  • MODALITY is a shorthand for the imaging modality used to obtain the data, e.g. sbem for serial blockface electron microscopy.
  • STAGE is a shorthand for the develpmental stage, e.g. 6dpf for six day post ferilisation.
  • ID is a number that distinguishes individual animals of a given modality and stage or distinguishes different set-ups for averaging based modalities like prospr.
  • REGION is a shorthand for the region of the animal covered by the data, e.g. parapod for the parapodium or whole for the whole animal.

Currently, the data contains the three modalities

  • sbem-6dpf-1-whole
  • prospr-6dpf-1-whole
  • fibsem-6dpf-1-parapod

Table storage

Derived attributes are stored in csv tables. Tables must be associated with a segmentation file segmentations/segmentation-name.xml All tables associated with a given segmentation must be stored in the sub-directory tables/segmentation-name. If this directory exists, it must at least contain the file default.csv with spatial attributes of the segmentation objects , which are necessary for the platybrowser table functionality.

If tables do not change between versions, they can be represented as soft-links to the old version.

Data generation

In addition to the data, the scripts for generating the derived data are also collected here. scripts/segmentation contains the scripts to generate the derived segmentations with automated segmentation approaches. The other derived data can be generated for new segmentation versions with the script update_platy_browser.py; make_initial_version.py was used to generate the initial data in /data/0.0.0.

Installation

TODO

BigDataServer

TODO