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Good day,
Thanks for developing this great tool. I want to use tangram to deconvolve each spot, but I have problems cropping using the same coordinates on the ImageContainer object and the data wit…
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When trying to read an HCS file on AWS S3 (e.g. `s3://bucket/file.ome.zarr`) the reader returns `Exception: Could not find first well`. Reading a specific well from the HCS file works fine (e.g. `s3:/…
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## Description
Hi,
Whenever we are trying in our FFPE Visium data to visualize cluster annotation in spatial context with [squidpy.pl.spatial_scatter()](https://squidpy.readthedocs.io/en/stable/a…
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Hi,
When I try to use sc.pl.spatial to plot the data with the parameter `edges = True`, I get the error `'list' object has no attribute 'set_zorder'` in line 511 of the code: `edge_collection.set_…
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Hello @nilseling ,
I am using imcRtools and cytomapper after running the whole single-cell and spatial IMC analysis using Python packages, such as Astir, Scanpy and Squidpy. I converted the resulte…
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In preparation for mini-sprint:
Discuss format of / guidelines for plotting functions.
MUCDK updated
2 years ago
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Hello, I am trying to read in multiomic data from the newly released 10X open source datasets: https://www.10xgenomics.com/resources/datasets/multiomic-integration-neuroscience-application-note-vi…
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Here to discuss the data generation step, which will be added in `datasets`
https://github.com/giovp/SingleCellOpenProblems/tree/master/openproblems/tasks/spatial_decomposition/datasets
Followi…
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Hi there,
I am trying to get the result from each permutation in gr.ligrec, which is the mean expression of the ligand receptor pair in all interaction clusters. I thought it would be stored in th…
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Hi,
I met a problem when I test the `GEM_toolkit.py` function with test data.
~~~R
cd ./GEM3D_toolkit-main/
vim test_gem2bfm.json
[
["/mnt/data/user_data/xiangyu/programme/GEM3D_toolkit-ma…