spatialdata-io
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The newest version (>4) of spaceranger supports nuclei/cell segmentation of VisiumHD data. I wonder if there are official on going plans to give support to this new feature? I am...
the steinbock reader uses `anndata.read` which has been removed in anndata 0.12 https://github.com/scverse/anndata/pull/1766 so it doesn't work with `anndata>=0.12`
Reader does not support cell segmentation of visium hd got after using latest spaceranger version 4
I am using the visiumhd data from the latest spaceranger pipeline that also contain segmented outputs but the reader doesnot support it unfortunately. It just work with bins Is there...
From user Jack on Zulip: > Does anyone know how to use spatialdata_io.stereoseq to read BGI's STOmics spatial transcriptomics data? Why is cell.cluster.h5ad required? The count output from SAW doesn't...
Fixes inconsistencies between the CLI interface (`__main__.py`) and reader APIs by ensuring all reader parameters are available through the command line interface. ## Problem The CLI exposed only a subset...
We have an in-house developed visualisation platform that can import multiple spatial biology ROIs/slides for spatial transcriptomics assays such as 10x Visium and Xenium. The current [spatialdata Visium reader](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/technology_visium.html) is...
Hi all, I managed to reproduce [this notebook](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/paper_reproducibility/lundeberg.ipynb) you also presented in the 2024 SpatialData paper, regarding Visium slide integration on a prostate from a unique patient. My main intention...
Dear, First, thank you for creating this package! It's been incredibly helpful in processing my CosMx data. I wanted to share a quick observation in case it helps anyone else....
As mentioned in [this issue](https://github.com/quentinblampey/spatialdata_xenium_explorer/issues/7), the `xenium_aligned_image` function assumes the image has 3 or 4 channels (i.e., typically, an H&E image). It would be great to expand it, as we...
Hi, I have installed the latest development version of spatialdata-io using **pip install git+https://github.com/scverse/spatialdata-io.git@main**. Then I tried the below code: from spatialdata_io import xenium sdata = xenium(path_to_xenium_folder) I get the...
