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Hi Lin,
Congrats on the paper. I was wondering where I could find the script for creating a gem file from my 10X visium data. I also looked into your repo with Colorectal cancer data and could not f…
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Hi David, could you also share the code to simulate Visium from Xenium?
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While extending SOPA for Visium HD data, @quentinblampey encountered a performance bottleneck with `aggregate()` that he could improve using pure `geopandas` code. Since we use `geopandas` internally,…
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Hi, I am working with the Visium HD colorectal cancer dataset. I have annotated a mask on the microscopic image with qupath and have it as a geoJSON file.
Could I please get instructions/ links to t…
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Hello
I followed tutorial https://github.com/zcang/COMMOT/blob/main/docs/notebooks/visium-mouse_brain.ipynb on one of the 10x visium based ST test data in our lab.
![image](https://github.com/…
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https://github.com/scverse/spatialdata-io/blame/bc17abc065c39e07d6b17affaf2c4b95adbaafea/src/spatialdata_io/readers/visium_hd.py#L357
Currently `visium_hd` function can't handle empty file prefixes…
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**Environment:**
- scResolve version: 0.1.0
- Operating System: Ubuntu 22.04
- Python version: Python 3.9
- Intel Cor i9, 64GB DDR5 + 66GB SWAP RAM
- Please check the installation script, as I ha…
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Hi,
Thank you for your excellent work on BayesSpace. I am currently attempting to implement BayesSpace with a 10x Visium data [link](https://www.10xgenomics.com/datasets/human-breast-cancer-ductal-…
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Right now, there is support for local .zarr stores and remote stores publically accessible via HTTP or S3.
Private remote stores are more difficult, as they need certain options or credentials that a…
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Hello!
I'm trying to run SCTransform on my Visium HD data, but I'm getting the error "Error: cannot allocate vector of size 80.7 Gb".
I have already increased the future.globals.maxSize, but it…