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Hi, I am working with the Visium HD colorectal cancer dataset. I have annotated a mask on the microscopic image with qupath and have it as a geoJSON file. Could...
As noticed by the 10x team, the link to the XOA file format [from the docs](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.xenium.html#spatialdata_io.xenium) is outdated. It should be replaced with the following one: https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/analysis/xoa-output-at-a-glance.
A new version of XOA has been released, which supports the new Xenium Prime 5K panels; from the [changelog](https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/release-notes/release-notes-for-xoa#v3-0) I believe that no modifications are required to for the `xenium()`...
Dear scverse Team, First of all, thank you for your effort on developping integrative frameworks for spatial transcriptomics data. Now, I'm analyzing MERFISH data using spatialdata. When I use cellpose...
This tries to solve #155. Lung_adc_demo ```python from spatialdata_io import macsima sdata = macsima('./Lung_adc_demo', subset=1000) sdata ``` ``` SpatialData object with: └── Images └── 'Lung_adc_demo': MultiscaleSpatialImage[cyx] (116, 1000, 1000), (116,...
As discussed in [here](https://github.com/scverse/spatialdata-io/pull/13), I made a few comments in the docstrings of the steinbock reader to improve documentation and possibly also improvements to the code. Also tagging @melonora here...
For using ISS data one needs to know the "round" and "channel" for each image. Is it within scope to represent this metadata in SpatialData? I could not see anything...
A reader to support reading data from the Miltenyi MACSima platform. It should support the published datasets: - [ ] [Liver Cell Atlas](https://livercellatlas.org/download.php) (old data stitched and already processed) -...
This pull request was created during the TheisLab Hackathon 2024 as part of a project to develop a cloud-based Spatial-DB. The primary goal is to ensure that when users upload...
