Closed will-moore closed 2 years ago
I assume this is closed waiting on https://github.com/ome/ngff/pull/67? It might be interesting to try the strategy here with the OME-XML from https://github.com/ome/ngff/issues/104
Try an OME-XML strategy from the bioformats2raw export? Or generate OME-XML via python? Not sure what "the strategy" means here?
I meant generate OME-XML from this plugin to match the specs in 104 which tie multiple images together into a single collection.
This PR replaces https://github.com/ome/omero-cli-zarr/pull/83 for export of a Dataset from OMERO:
This will create a top-level group, named after the Dataset ID:
1.zarr
The group metadata listsimages
using their name as a path:NB: as noted on PR above, some characters in image names break this, e.g.
/
,[
,]
so need to handle them.Recent test export using commit 8dc4707 below is hosted at https://minio-dev.openmicroscopy.org/idr/v0.3/datasets/idr0043/13901.zarr and can be viewed in vizarr but it not very reliable (see https://github.com/hms-dbmi/vizarr/pull/124#issuecomment-934226522)