squidpy
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Spatial Single Cell Analysis in Python
Dear all, I tried to follow this workflow (https://squidpy.readthedocs.io/en/stable/external_tutorials/tutorial_vizgen_mouse_liver.html) for the Human Liver cancer dataset (https://info.vizgen.com/ffpe-showcase) instead. But when using squidpy.read.vizgen(), the obsm and var from the AnnData object are...
## Description When the `groups`parameter is specified in `sq.pl.spatial_segment` the cells that are plotted are not the cells where `adata.obs[color].isin(groups)`. For example with the `mibitof` dataset below, when `groups =...
CODEX
Hello, thanks for an awesome package! I am currently trying to extract image features within a segmentation mask and here is my set up so far: `mpif = tiff.imread('mpif_cropped.ome.tiff')` `mask...
Hello, Thank you for this amazing tool! It has been so helpful in dealing with spatial data, especially in a way that is reasonable in terms of memory and resources....
## Example data in figshare could not be downloaded ```python >>> import squidpy as sq >>> adata = sq.datasets.slideseqv2() Traceback (most recent call last): File "", line 1, in File...
## Description Hi, When I ran the code ``` img=sq.im.ImageContainer(adata_st.uns['spatial']['T91']["images"]['hires'],library_id='T91') viewer = img.interactive(adata_st) ``` I only get a black GUI, I'm not sure is it correlated with my WSL2-Ubuntu20.04? Could...
Hello, I have a question about this tutorial: https://squidpy.readthedocs.io/en/latest/notebooks/examples/plotting/plot_segment.html. In this tutorial, you have plotted fibroblast and epithelial clusters at once on two FOVs: But when these are plotted without...
## Description Calculating co-occurrences I noticed some inf and nan values in the outcome and while looking into it I saw Issue #689 and tried to reduce n_splits to 1....
Hi, good day. Thank you for the very nice package. I have an issue loading the Nanostring CosMx dataset: [Nanosctring CosMx dataset](https://nanostring.com/products/cosmx-spatial-molecular-imager/human-frontal-cortex-ffpe-dataset/?mkt_tok=NzAwLUpZRi0xNzEAAAGOSsg2hyHYrN92QqO6ubV-6rcqX2TYhdJlPmIMX7YcRgCxbHZxX0GUkA08o1-A8i38k1KFyzk8LR_1v0i9mQg1OqxS7p520rcuRbPYQ_6tDZfMkQ) Here is the error I am getting: Traceback...
Hello, I'm running `sq.gr.nhood_enrichment(adata, cluster_key=label_name, numba_parallel=False, n_jobs=1, backend=None)` but multiprocessing still seems to get at least initialized somehow, which I know because I'm *calling* Squidpy from a program that's already...
