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Commit b76d9761 authored by Constantin Pape's avatar Constantin Pape
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Merge branch 'dev' of https://git.embl.de/tischer/platy-browser-tables into dev

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# platy-browser-tables
# platy-browser-data
Data and data-generation for the [platybrowser](https://github.com/embl-cba/fiji-plugin-platyBrowser).
......@@ -20,6 +20,19 @@ For a given version `X.Y.Z`, the data is stored in the directory `/data/X.Y.Z/`
- `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
......@@ -27,8 +40,7 @@ Derived attributes are stored in csv tables. Tables must be associated with a se
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.
If tables do not change between versions, they can be represented as soft-links to the old version.
## Data generation
......@@ -42,3 +54,8 @@ The other derived data can be generated for new segmentation versions with the s
## Installation
TODO
## BigDataServer
TODO
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