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Forked from Christian Tischer / platy-browser-data
301 commits behind the upstream repository.
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Constantin Pape authored
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data/0.0.0
scripts
test/attributes
.gitignore
README.md
environment.yaml
make_initial_version.py
update_platy_browser.py
README.md

platy-browser-tables

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.

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.

TODO think about linking to previous table version. Simplest option would be to replace the directory tables/segmentation-name with a text file that contains the absolute path to the previous table 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