Description

Currently Webknossos annotations are in the *.wkw format. We should create scripts to export and convert these annotations to either OME-Zarr or NIfTI-Zarr. We have decided to select the output format to match the base imaging layer(s) so that the orientation is preserved. We can use either the wkcuber or webknossos Python libraries.

Goals

• Determine additional metadata in the Webknossos annotation files (e.g. annotator name, mapping of segmentation names)
• Create a script to perform the following operations:
  • Determine the base imaging layer(s) format of the corresponding Webknossos dataset (i.e. OME-Zarr or NIfTI-Zarr)
  • Export Webknossos annotation as a OME-Zarr file
  • Export Webknossos annotation as a NIfTI-Zarr file
  • Add the above Webknossos metadata to the exported file

Thank you.