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Currently, we can only transfer from instances that run the same version. We need to replace `laminlabs/cellxgene` with a development instance so that we can keep tests passing.
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I am analysing a Xenium dataset. I want to use the Crop function to create a new field of view.
The following code works in RStudio:
Minimal reproducible example, e.g. using the 10X Xenium colo…
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## Describe the bug
Calling `open_soma()` returns an error `3137 illegal hardware instruction`
## To Reproduce
### Setup
```
python3.11 -m venv venv
source venv/bin/activate
pip install -U ce…
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### Please make sure these conditions are met
- [X] I have checked that this issue has not already been reported.
- [X] I have confirmed this bug exists on the latest version of scanpy.
- [X] (op…
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## Description
This would be similar to `cellxgene_census.get_anndata` and reduce the amount of code users have to write.
**Current**
```
cell_metadata = census["census_data"]["homo_sapiens"].…
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**Describe the bug**
Using the SOMA `IntIndexer` is causing a memory leak which isn't present when using the regular Pandas indexer.
**To Reproduce**
```
import gc
import numpy as np
impor…
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Thanks for ur great work! The paper and docs have mentioned that the whole-human dataset consists of 33M cell 's data. And u have given some shell scripts to crawl the data from CellxGene. Actually,…
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This is for the `pyarrow` CVE. @bkmartinjr has verified we don't use the vulnerable code path, but, it's good optics for us to update.
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### Need
Atlases often have multiple components. These will be h5ad files (AnnData) that integrate different source datasets.
They may vary by tissue, disease, or assay, for example.
We must su…