spatialdata
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An open and interoperable data framework for spatial omics data
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...
updates: - [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2) - [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0) - [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.1...v0.4.3)
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Hi, Thank you for the spatialdata package. I'm just wondering if it's possible to subset our spatialdata object directly by a list of cell ids? I couldn't find it in...
Hi developers, Thanks for the amazing framework. I am using the framework to extract non-linear features from image patches of visium samples. When performing some QC on the data, I...
Hi, I'm trying to perform a polygon_query() on a Xenium object: ``` SpatialData object with: ├── Images │ ├── 'he_image': MultiscaleSpatialImage[cyx] (3, 33558, 57706), (3, 16779, 28853), (3, 8389, 14426),...
The new releases of `spatial_image` and `multiscale_spatial_image` use these the base classes `DataArray` and `DataTree`. We need to: - [ ] add support for these classes - [ ] remove...
Closes #186 Closes #496 Closes #498 Support for incremental io operations. New features: - [x] ability to save additional elements to disk after the `SpatialData` object is created - [x]...
Hi, Thanks for developing such an exciting tools. I'm trying the process of annotating regions using napari software follow the tutorial https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/napari_rois.html, but I found some results do not make...
Fixes scverse/spatialdata-plot#249 Please see the above `spatialdata-plot` issue for a problem description. This is just a draft of how this issue could be addressed. I could see several different routes...
