squidpy
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Spatial Single Cell Analysis in Python
## Description Hi All, I've encountered an issue with passing a scaling factor for feature calculations. More specifically, whenever a scale value is passed that is not equivalent to the...
## Description was unable to load datasets which are included in squidpy (visium_hne_adata()) ... ## Minimal reproducible example import squidpy as sq adata = sq.datasets.visium_hne_adata() img = sq.datasets.visium_hne_image() ```python ......
taking inspiration from what it is done in scirpy: [scverse/scirpy@main/.github/workflows/test-tutorials.yaml](https://github.com/scverse/scirpy/blob/main/.github/workflows/test-tutorials.yaml?rgh-link-date=2023-06-15T15%3A18%3A41Z) it would be useful to have a way to test the examples in CI in order to keep track on...
## Description Trouble using vizgen data with sq.read.vizgen(). Function is expected 8 columns in metadata file mine has 9 ## Minimal reproducible example ```python adata = sq.read.vizgen( path=data_path, counts_file=os.path.join(data_path,section,file_path,cbg_file), meta_file=os.path.join(data_path,section,file_path,meta_file),...
## Description I might be overlooking it, but is it possible to delete a layer from an imagecontainer object? I don't want to save all the layers that I created...
I am re-opening this issue because I am still having problems running squidpy.gr.co_occurrence() with n_splits>1. I noticed that this has been previously discussed [here](https://github.com/scverse/squidpy/issues/582) and was closed without resolution. When...
According to [https://scikit-image.org/docs/stable/api/skimage.measure.html#skimage.measure.regionprops](https://scikit-image.org/docs/stable/api/skimage.measure.html#skimage.measure.regionprops), `segmentation_area_mean` returned from `sq.im.calculate_image_features` means `number of pixels of the region scaled by pixel-area.`. But I am confused by the `mean`, does it scaled by the total...
Hi, I am trying to use the example slideseqv2 data in Squidpy, starting from raw counts. However, the returned adata has a raw.X but it is actually the preprocessed version...
Hi everyone, I analyzed Visium spatial transcriptomics data using squidpy. When using "spatial_scatter", is it possible to not show specific dots with a gene expression leven below a certain threshold....
Hi, I specified `segmented_custom` in the following code ``` sq.im.segment(img=img2, layer="image_smooth", channel=None, method=cellpose_he, channel_cellpose=0, flow_threshold=1) #FINAL COUNTING sq.im.calculate_image_features( adata, img2, #layer="image", layer=seg_layer, #layer='segmented_watershed', features="segmentation", key_added="segmentation_features", #https://scikit-image.org/docs/stable/api/skimage.measure.html#skimage.measure.regionprops features_kwargs={ "segmentation": { "label_layer":...