Data and data-generation for the [platybrowser](https://github.com/embl-cba/fiji-plugin-platyBrowser).
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/`
...
@@ -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.
-`segmentations`: Segmentation volumes derived from the image data. Only xml files.
-`tables`: CSV tables with attributes derived from image data and segmentations.
-`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
### Table storage
...
@@ -27,8 +40,7 @@ Derived attributes are stored in csv tables. Tables must be associated with a se
...
@@ -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`.
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 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
If tables do not change between versions, they can be represented as soft-links to the old version.
text file that contains the absolute path to the previous table version.
## Data generation
## Data generation
...
@@ -42,3 +54,8 @@ The other derived data can be generated for new segmentation versions with the s
...
@@ -42,3 +54,8 @@ The other derived data can be generated for new segmentation versions with the s
