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adjusted docstrings in steinbock reader py file #165

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adjusted docstrings in steinbock reader py file #165

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adjusted docstrings in steinbock reader py file
LukasHats Jun 27, 2024
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 27, 2024
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18 changes: 18 additions & 0 deletions src/spatialdata_io/readers/steinbock.py
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Expand Up @@ -33,6 +33,24 @@ def steinbock(

- `Steinbock pipeline <https://bodenmillergroup.github.io/steinbock/latest/>`_.

Current mandatory outputs of the Steinbock toolkit
----------
- one comprehensive anndata object labeled as 'cells.h5ad' in the main working directory
- 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
(https://bodenmillergroup.github.io/steinbock/latest/cli/preprocessing/)

The andata tables, masks and ome.tiffs have to be named accordingly so the
spatialdata.io steinbock reader correctly assigns all instances.


Parameters
----------
path
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