spatialdata-io
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Hi, after having updated my spatialdata-io from version 0.1.4 to 0.1.7, I am having an issue with the cosmx reader to create a spatialdata object. Using the same data that...
After segmentation with cellpose, I ran Xenium Ranger 3.0.1.1 `xeniumranger import-segmentation --id=my_ID \ --xenium-bundle=$DIR/outs \ --nuclei=$DIR/outs/mask_nuclei.ome_cp_masks.tif \ --cells=$DIR/outs/mask_cells.ome_cp_masks.tif ` When I try to read the output folder with spatialdata_io (0.1.7.dev5+g82ff327),...
It adds a new `output_path` parameter in a reader's function that allows to save every element of the spatialdata object as soon as it's created. This frees up part of...
Some Xenium datasets deposited in GEO lack h5 file format and instead decided to upload market format. For example: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM8253804 Of course it is possible to ask the authors to...
We currently have a the custom implementation for reading matrices (copied from `scanpy`) in https://github.com/scverse/spatialdata-io/blob/main/src/spatialdata_io/readers/_utils/_read_10x_h5.py. I would remove that code and use directly `scanpy`, which is already a dependency. I...
Hello, Segmentation of nuclei on VisiumHD H&E image might require (at least for StarDist segmentation model) to have the micron per pixel information (since pre trained models can be trained...
Hello everyone, I had issues setting up my spatialdata environment. My environment is super naked as I had several other issues with other packages i.e. numpy. I figured out a...
Hi, SpaceRanger can be run on Visium HD data without a full resolution microscopy image, and only the CytAssist image. This will create a metadata_json with `"microscope_colrow_to_spot_colrow": null`, which will...
