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ome / napari-ome-zarr

A napari plugin for zarr backed OME-NGFF images
https://www.napari-hub.org/plugins/napari-ome-zarr
BSD 3-Clause "New" or "Revised" License
27 stars 21 forks source link

Labels should be opened as label layer #35

Closed constantinpape closed 2 years ago

constantinpape commented 2 years ago

After fixing the issues with my data observed in #33. The labels are now loaded by the plugin. However they are loaded as image layer: image

It would make more sense to load them as label layer instead. Note that this is particularly annoying right now since it's not possible to convert them into a label layer due to #34.

will-moore commented 2 years ago

Can you try napari https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/idr0079A/9836998.zarr, which is an example with labels that show up as labels for me. Can you share the data you're viewing above?

constantinpape commented 2 years ago

Can you try napari https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/idr0079A/9836998.zarr, which is an example with labels that show up as labels for me.

Yes, that opens it as labels layer for me too.

Can you share the data you're viewing above?

I uploaded the data here: https://oc.embl.de/index.php/s/wfpdHpgHseGUTYK. It is from the example here: https://github.com/ome/ome-ngff-prototypes/tree/main/workflows/spatial-transcriptomics-example

constantinpape commented 2 years ago

I found the likely culprit: https://github.com/ome/ngff/issues/109 (I have used snake case, i.e. image_label.) Will double check this now.

constantinpape commented 2 years ago

Yes, this fixes the issue.