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src/spatialdata_io/readers/steinbock.py

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