spatialdata-io
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scverse
Hello, I'm reaching out for a request more than help. Would anyone mind sharing their python environment with me, like a yml file or something of the like. I'm having...
I ran `xenium()` with default parameters on official data from 10x Genomics (such as https://www.10xgenomics.com/datasets/ffpe-human-breast-with-custom-add-on-panel-1-standard). However, I noticed that when I plotted the H&E image using the `spatialdata-plot` package, there...
Features include: - Dask array conversion for flexible chunking - VRAM check to ensure memory sufficiency - Zarr-backed optimization check for efficient handling of large images This PR is part...
> Hi, > We are using Stereo-seq a lot. It's more common to operate on the bin but not the cell_circles for most of the stereoseq users, because the cell...
> Thanks for the clarification. That makes sense. > > One small detail. Should not the elements in `Tables` be renamed as well? Right now they are not (see above)....
Hi @LucaMarconato . Thanks for developing spatialdata-io, it is super helpful in processing spatial data. I wanted to use this package to process my dbit-seq data, but I had trouble...
The merscope image files that I use are currently quite big, and it is often useful for me to only select specific stains. Currently it is hard coded in the...
Additional fixes to support the seqFISH v2 file format. ## Changelog - improved parsing of OME XML metadata - automatically parsing images as multiscale when they are larger than a...
Hello, I am running one of the tutorials and I have installed both spatialdata and spatialdata_io packages, but there is an error importing spatialdata_io. Could you help? Thank you very...
This commit seems to solve my issue reported here: https://github.com/scverse/spatialdata-io/issues/208 Is there a reason why only polygons from ```z_index = 0 ``` are kept? By default the reader select plane...