From 53981ac98ce1b09e9dacbffc014ed32bd229cf5b Mon Sep 17 00:00:00 2001 From: Lukas Hatscher Date: Thu, 27 Jun 2024 12:21:29 +0000 Subject: [PATCH 1/2] adjusted docstrings in steinbock reader py file --- src/spatialdata_io/readers/steinbock.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/src/spatialdata_io/readers/steinbock.py b/src/spatialdata_io/readers/steinbock.py index 69cd5e40..848d97b6 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 From 7811298627f31ca253444b66a58b6c46dc9eb772 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 27 Jun 2024 12:32:42 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/spatialdata_io/readers/steinbock.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/spatialdata_io/readers/steinbock.py b/src/spatialdata_io/readers/steinbock.py index 848d97b6..adb9770b 100644 --- a/src/spatialdata_io/readers/steinbock.py +++ b/src/spatialdata_io/readers/steinbock.py @@ -39,15 +39,15 @@ def steinbock( - 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 + 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 + The andata tables, masks and ome.tiffs have to be named accordingly so the spatialdata.io steinbock reader correctly assigns all instances.