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[pre-commit.ci] auto fixes from pre-commit.com hooks
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pre-commit-ci[bot] committed Jun 27, 2024
1 parent 53981ac commit 7811298
Showing 1 changed file with 7 additions and 7 deletions.
14 changes: 7 additions & 7 deletions src/spatialdata_io/readers/steinbock.py
Original file line number Diff line number Diff line change
Expand Up @@ -39,15 +39,15 @@ def steinbock(
- an 'ome' folder containing the steinbock ome.tiff exported tiff images
- masks directory labeled as either 'masks_deepcell' or 'masks_ilastik'
Users have to carefully construct the andata object with steinbock using the images.csv table.
Constructing the anndata object without the images.csv table will leave the anndata without
'adata.obs.images' which will subsequently result in an error (see line 99)
Therefore, currently users are adviced to start their steinbock analyses from .mcd files.
A possible workaround for this would be to handcraft the images.csv table according to steinbock format
if users want to start from tiff images in steinbock
Users have to carefully construct the andata object with steinbock using the images.csv table.
Constructing the anndata object without the images.csv table will leave the anndata without
'adata.obs.images' which will subsequently result in an error (see line 99)
Therefore, currently users are adviced to start their steinbock analyses from .mcd files.
A possible workaround for this would be to handcraft the images.csv table according to steinbock format
if users want to start from tiff images in steinbock
(https://bodenmillergroup.github.io/steinbock/latest/cli/preprocessing/)
The andata tables, masks and ome.tiffs have to be named accordingly so the
The andata tables, masks and ome.tiffs have to be named accordingly so the
spatialdata.io steinbock reader correctly assigns all instances.
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