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src/spatialdata_io/readers Expand file tree Collapse file tree Original file line number Diff line number Diff line change @@ -33,6 +33,24 @@ def steinbock(
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3434 - `Steinbock pipeline <https://bodenmillergroup.github.io/steinbock/latest/>`_.
3535
36+ Current mandatory outputs of the Steinbock toolkit
37+ ----------
38+ - one comprehensive anndata object labeled as 'cells.h5ad' in the main working directory
39+ - an 'ome' folder containing the steinbock ome.tiff exported tiff images
40+ - masks directory labeled as either 'masks_deepcell' or 'masks_ilastik'
41+
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
48+ (https://bodenmillergroup.github.io/steinbock/latest/cli/preprocessing/)
49+
50+ The andata tables, masks and ome.tiffs have to be named accordingly so the
51+ spatialdata.io steinbock reader correctly assigns all instances.
52+
53+
3654 Parameters
3755 ----------
3856 path
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