diff --git a/src/spatialdata_io/readers/steinbock.py b/src/spatialdata_io/readers/steinbock.py index 69cd5e40..adb9770b 100644 --- a/src/spatialdata_io/readers/steinbock.py +++ b/src/spatialdata_io/readers/steinbock.py @@ -33,6 +33,24 @@ def steinbock( - `Steinbock pipeline `_. + 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