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src/spatialdata_io/readers Expand file tree Collapse file tree Original file line number Diff line number Diff line change @@ -39,15 +39,15 @@ def steinbock(
3939 - an 'ome' folder containing the steinbock ome.tiff exported tiff images
4040 - masks directory labeled as either 'masks_deepcell' or 'masks_ilastik'
4141
42- Users have to carefully construct the andata object with steinbock using the images.csv table.
43- Constructing the anndata object without the images.csv table will leave the anndata without
44- 'adata.obs.images' which will subsequently result in an error (see line 99)
45- Therefore, currently users are adviced to start their steinbock analyses from .mcd files.
46- A possible workaround for this would be to handcraft the images.csv table according to steinbock format
47- if users want to start from tiff images in steinbock
42+ Users have to carefully construct the andata object with steinbock using the images.csv table.
43+ Constructing the anndata object without the images.csv table will leave the anndata without
44+ 'adata.obs.images' which will subsequently result in an error (see line 99)
45+ Therefore, currently users are adviced to start their steinbock analyses from .mcd files.
46+ A possible workaround for this would be to handcraft the images.csv table according to steinbock format
47+ if users want to start from tiff images in steinbock
4848 (https://bodenmillergroup.github.io/steinbock/latest/cli/preprocessing/)
4949
50- The andata tables, masks and ome.tiffs have to be named accordingly so the
50+ The andata tables, masks and ome.tiffs have to be named accordingly so the
5151 spatialdata.io steinbock reader correctly assigns all instances.
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