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README.md 3.17 KiB

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.