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Hi,
Thanks for developing this great tool.
I'm running into an error in **LoadH5Seurat()** step, stated that: _Error: Missing required datasets 'levels' and 'values'_.
My data was downloaded …
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Im trying to find DEGs between the leiden clusters use ov.single.cosg
Here is a simple example.
`adata`
```
AnnData object with n_obs × n_vars = 117399 × 21054
obs: 'sample', 'n_genes_by_co…
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Hey, I'm trying to use this tool, but the environment file is not very specific on what numpy version to use and so it installs numpy 2.0 as default; However, there are pieces of code that have been s…
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Writing MERSCOPE data may use a lot of RAM. This is because the `.tif` image chunks are not detected when using `imread` from `dask_image`, so the full image has to be loaded during image writing.
…
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Hi,
I follow the instructions from the [scvi-tools tutorial || Quick START TUTORIAL || Mapping human lymph node cell types to 10X Visium with Cell2location] and download all required package of ce…
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scib is not compatible with scanpy 1.10.0 because the symbol `deprecated_arg_names` has been removed from scanpy (in PR https://github.com/scverse/scanpy/pull/2702 )
This leads to build failures su…
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Hi,
I am trying to get an AnnData object out of a SpatialData object created with `spatialdata_io.visium(...)`:
```python
import spatialdata_io
from spatialdata_io.experimental import to_legacy_…
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Hi @quentinblampey,
I was wondering if there's a good reason to pin anndata to 0.8? A lot of new features and bugfixes have been added since then and I can't read `zarr` files that were generated …
grst updated
7 months ago
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Hi,
Thanks for your great work in Spatial omics filed!
I used SpatialData to integrate two images and following the tutorial "Use landmark annotations to align multiple -omics layers". Everything we…