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Hi, thanks for implementing this fantastic tool!
I'm wondering if the Visium heart dataset might be corrupted because the samples `GT_IZ_P9` and `GT_IZ_P9_rep2` (ACH0012 and ACH0013) appear to be ide…
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How do I bypass this error?
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 't': cannot allocate vector of size 722.0 Gb
Calls: Spa…
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The visium_hd function from spatialdata-io is currently returning an error importing the images from spaceranger output.
This is the error I am running into
```
File /data/williamsd7/cond…
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Hello,
I am using Seurat to analyze my Visium data, and have noticed dramatic differences between the SCT result between v4 and v5. Everything is detailed below - but my main question is **in v5 do…
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I have pre-annotated regions in QuPath and exported them as geoJSON files. Can these be loaded directly or converted in some way so that I may perform spatially-aware DE of my Visium data?
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Trying to use BPCells to help with smoother analysis of Visium HD data but keep getting errors.
localdir visium_data
> # Convert to BPCells format
> expr_matrix expr_matrix_int
> write_ma…
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# Changelog
* uns (Dataset Metadata)
* Updated the requirements for `spatial` to include descendants of _Visium Spatial Gene Expression_.
* Updated the requirements for spatial['is_single']…
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# Changelog
## X (Matrix Layers)
- Updated Visium Spatial Gene Expression table row to **Descendants** of Visium Spatial Gene Expression
- Added matrix requirements for Visium CytAssist Spatial…
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I've encountered two issues when using the package:
1. Missing Sample Prefix in Output Files:
Our output files do not include a sample prefix, which makes an error when reading the feature_slice.h…
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## Description
When `tissue_positions.csv` rather than `tissue_positions_list.csv` is in the spatial directory for a Visium dataset, the resulting AnnData object has:
- NaN in adata.obs array_row, a…