GitHub / scverse/spatialdata issues and pull requests
#951 - Geometry encoding parameter for shapes
Pull Request -
State: open - Opened by keller-mark 29 days ago
#950 - Error in aggregate over Image2DModel by Labels2DModel when transform is more complex than translation
Issue -
State: open - Opened by m-albert 30 days ago
- 2 comments
#949 - Reported issue with bounding box query and rotated images
Issue -
State: open - Opened by LucaMarconato about 1 month ago
- 1 comment
Labels: method: query
#948 - When transforming DataTree elements, discard scales resulting in zero shape
Pull Request -
State: open - Opened by m-albert about 1 month ago
- 1 comment
#947 - Error when applying `spatialdata.transform` to multiscale images (related to scale handling)
Issue -
State: open - Opened by m-albert about 1 month ago
#946 - Filter Operations on Label2DModel and Shape
Pull Request -
State: open - Opened by selmanozleyen about 1 month ago
- 1 comment
#945 - Fix typo
Pull Request -
State: closed - Opened by Zethson about 1 month ago
- 1 comment
#944 - restore option to compress raster
Pull Request -
State: open - Opened by melonora about 2 months ago
- 2 comments
#943 - Alignment of points/shapes with labels/images in spatialdata from COSMX
Issue -
State: closed - Opened by joaolsf about 2 months ago
- 1 comment
#942 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: open - Opened by pre-commit-ci[bot] 2 months ago
- 1 comment
#941 - Error import spatialdata
Issue -
State: closed - Opened by Yijia-Jiang 2 months ago
- 1 comment
#940 - Add dedicated API/CLI for validation of on-disk data
Issue -
State: open - Opened by LucaMarconato 2 months ago
#939 - Add type hint when get a SpatialElement item
Pull Request -
State: closed - Opened by quentinblampey 2 months ago
- 2 comments
#938 - write_element and delete_element_from_disk are very slow when SpatialData object contains large number of elements
Issue -
State: open - Opened by mjheid 2 months ago
- 1 comment
#937 - Read xenium data get TypeError: unhashable type: 'list'
Issue -
State: open - Opened by henryccl 2 months ago
- 1 comment
#936 - get_centroids() slow on on labels elements
Issue -
State: open - Opened by cavenel 2 months ago
#935 - Helper function to sanitize tables
Pull Request -
State: closed - Opened by timtreis 3 months ago
- 3 comments
#934 - Utils function to sanitise obs columns
Issue -
State: closed - Opened by timtreis 3 months ago
#933 - Deal with the case when `.attrs`/`.uns` are not JSON-serializable
Issue -
State: open - Opened by LucaMarconato 3 months ago
#932 - Large spatial transcriptomics datasets best practices
Issue -
State: open - Opened by KalinNonchev 3 months ago
#931 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 3 months ago
- 1 comment
#930 - add datashader dependency
Pull Request -
State: closed - Opened by LucaMarconato 3 months ago
- 1 comment
#929 - irregular chunking
Issue -
State: closed - Opened by Lem-P 5 months ago
- 6 comments
#928 - fix docs urls
Pull Request -
State: closed - Opened by LucaMarconato 3 months ago
- 1 comment
Labels: release-ignore
#927 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 3 months ago
- 1 comment
#926 - Uncaught error during pretty print
Issue -
State: open - Opened by falexwolf 4 months ago
- 1 comment
Labels: bug 🚨
#924 - sd.concatenate throws ValidationError on queried sdatas
Issue -
State: open - Opened by fbnrst 4 months ago
#923 - Integration Testing CI Test Failure on python 3.12
Issue -
State: open - Opened by scverse-bot 4 months ago
#922 - Integration Testing CI Test Failure on python 3.11
Issue -
State: open - Opened by scverse-bot 4 months ago
#921 - Account for the padding shift during vectorization + use multipolygon
Pull Request -
State: closed - Opened by quentinblampey 4 months ago
- 4 comments
#920 - Keep polygon interior during vectorization
Issue -
State: open - Opened by quentinblampey 4 months ago
#919 - Added parameter to `sd.concatenate` to control whether to merge coordinate systems with the same name
Pull Request -
State: open - Opened by timtreis 4 months ago
- 2 comments
#918 - sd.concatenate doesn't apply suffix to coordinate systems
Issue -
State: open - Opened by timtreis 4 months ago
Labels: enhancement ✨, method: concatenate, release-added
#917 - [Feature Request] Convert from LabelsModel to ShapesModel
Issue -
State: open - Opened by lguerard 4 months ago
#914 - Remove reference cycle within SpatialData to fix memory leak in bounding_box_query
Pull Request -
State: open - Opened by nickodell 4 months ago
- 1 comment
#913 - Geopandas benchmarks
Pull Request -
State: open - Opened by aeisenbarth 4 months ago
- 1 comment
#912 - module 'spatialdata' has no attribute 'match_sdata_to_table'
Issue -
State: closed - Opened by bellenger-l 4 months ago
- 10 comments
#911 - cannot import spatialdata
Issue -
State: open - Opened by bozhangstat 4 months ago
- 2 comments
#910 - `render_points` with column coloring throws error when there are too many points
Issue -
State: open - Opened by ziyuanzhao2000 4 months ago
#907 - [scverse hackathon] cloud future
Pull Request -
State: open - Opened by ap-- 5 months ago
- 1 comment
#906 - Rename SpatialData elements
Issue -
State: open - Opened by Fritze 5 months ago
- 1 comment
#899 - Restoring conda support
Issue -
State: closed - Opened by LucaMarconato 5 months ago
- 3 comments
#898 - Is there a way to subset cell_boundaries using an AnnData table?
Issue -
State: closed - Opened by Pancreas-Pratik 5 months ago
- 4 comments
#896 - Resolve AnnData FutureWarnings `The dtype argument is deprecated`
Pull Request -
State: closed - Opened by Zethson 5 months ago
- 1 comment
Labels: release-fixed
#894 - Added `filter_table_by_query`
Pull Request -
State: open - Opened by srivarra 5 months ago
- 6 comments
#892 - add trademark
Pull Request -
State: closed - Opened by melonora 5 months ago
- 1 comment
Labels: release-ignore
#891 - Add encoding type and version to write_zarr
Pull Request -
State: closed - Opened by Zethson 5 months ago
- 3 comments
#889 - Docs: replace all links pointing `latest` docs to `stable` docs
Issue -
State: closed - Opened by LucaMarconato 5 months ago
- 1 comment
Labels: docs 📜, priority: high
#888 - Tutorial Technology Visium HD fails due to coordinate system
Issue -
State: closed - Opened by pcm32 5 months ago
- 2 comments
#886 - Image2DModel.parse() forgetting about scale_factors if chunking
Issue -
State: open - Opened by josenimo 5 months ago
- 2 comments
#884 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 5 months ago
- 2 comments
#883 - pin numba to earlierst version supporting python 3.10
Pull Request -
State: closed - Opened by giovp 5 months ago
- 1 comment
Labels: release-fixed
#881 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 6 months ago
- 1 comment
#877 - Replace pip with uv for test workflow
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 6 comments
Labels: release-changed
#876 - fix max chunk size calculation
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 1 comment
Labels: release-fixed
#874 - Add warning (raster models) when large chunks are detected
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 2 comments
Labels: release-added
#873 - fix suffix concatenate when each table annotates > 1 elements
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 1 comment
Labels: release-fixed
#871 - Fix bug custom region_key concatenate
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 1 comment
Labels: release-fixed
#869 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 6 months ago
- 1 comment
#868 - Add 2025 roadmap; remove legacy example (design doc)
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 1 comment
Labels: release-ignore
#867 - Update README.md: conda not available
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 1 comment
Labels: release-ignore
#864 - Fix bug join operation with non-annotating table
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 1 comment
Labels: release-fixed
#861 - Fix rechunk bug after spatial query
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 2 comments
Labels: release-fixed
#858 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 6 months ago
- 1 comment
#857 - Revert "Update pyproject.toml"
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 1 comment
Labels: release-ignore
#853 - Fix JoinTypes.__dict__ empty python 3.13
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 2 comments
Labels: release-fixed
#851 - Use Ruff for code formatting
Pull Request -
State: closed - Opened by Zethson 6 months ago
- 1 comment
Labels: release-ignore
#849 - Specify NGFF 0.6-dev in output data
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 5 comments
Labels: release-changed
#848 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 6 months ago
- 1 comment
#841 - Docker automatic build
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 2 comments
Labels: release-added
#840 - Restore support for Python >=3.13
Pull Request -
State: closed - Opened by LucaMarconato 6 months ago
- 1 comment
Labels: release-fixed
#837 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 6 months ago
- 1 comment
#833 - fix index error left join
Pull Request -
State: closed - Opened by melonora 7 months ago
- 1 comment
Labels: release-fixed
#832 - fix index cannot be reshaped with inner join
Pull Request -
State: closed - Opened by melonora 7 months ago
- 1 comment
Labels: release-fixed
#830 - Add autodoc_default_options to inherit docstrings
Pull Request -
State: closed - Opened by quentinblampey 7 months ago
- 1 comment
Labels: release-ignore
#826 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 7 months ago
- 1 comment
#822 - Fix bug with join with duplicate obs indices
Pull Request -
State: closed - Opened by melonora 7 months ago
- 3 comments
Labels: release-fixed
#821 - Unable to save subsetted Xenium `sdata` to `.zarr`
Issue -
State: closed - Opened by christinedien 7 months ago
- 8 comments
#820 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 7 months ago
- 1 comment
#819 - Prettier mismatch between local and remote
Pull Request -
State: closed - Opened by LucaMarconato 7 months ago
- 4 comments
Labels: release-ignore
#818 - add support for `layer` selection in `get_values()` method
Pull Request -
State: closed - Opened by Sonja-Stockhaus 7 months ago
- 2 comments
#817 - improved release instructions and workflow
Pull Request -
State: closed - Opened by LucaMarconato 7 months ago
- 2 comments
Labels: release-ignore
#814 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 7 months ago
- 1 comment
#813 - fix join non matching table
Pull Request -
State: closed - Opened by melonora 7 months ago
- 1 comment
Labels: release-fixed
#811 - `rasterize_bins()` can now produce a labels element
Pull Request -
State: closed - Opened by ArneDefauw 8 months ago
- 2 comments
#806 - `get_attrs()`: helper function to return keys in the `sdata.attrs` slot in an specific format
Pull Request -
State: closed - Opened by timtreis 8 months ago
- 1 comment
Labels: enhancement ✨
#787 - bug with 3d data test in transform_to_data_extent
Pull Request -
State: closed - Opened by LucaMarconato 9 months ago
- 3 comments
Labels: release-fixed
#785 - Improved docs: adding glossary + refactor API reference display
Pull Request -
State: closed - Opened by quentinblampey 9 months ago
- 2 comments
#778 - Added a spatialdata-io mirror
Pull Request -
State: closed - Opened by quentinblampey 9 months ago
- 3 comments
#777 - add warning when running bounding box query if points is present
Pull Request -
State: closed - Opened by BioinfoTongLI 9 months ago
- 1 comment
Labels: release-fixed
#765 - Partial reading
Pull Request -
State: closed - Opened by aeisenbarth 9 months ago
- 2 comments
Labels: release-added
#703 - More robust name validation
Pull Request -
State: closed - Opened by aeisenbarth 11 months ago
- 8 comments
#631 - Improvement to the docs
Issue -
State: open - Opened by LucaMarconato about 1 year ago
- 6 comments
Labels: docs 📜
#627 - allow filtering by ids
Pull Request -
State: closed - Opened by melonora about 1 year ago
- 5 comments
Labels: release-added
#626 - Draft SpatialData.filter()
Pull Request -
State: closed - Opened by aeisenbarth about 1 year ago
- 14 comments
#419 - Remove `region` from `adata.uns['spatialdata_attrs']`
Issue -
State: open - Opened by LucaMarconato over 1 year ago
- 1 comment
Labels: topic: table
#417 - general fixes to adapt table model
Pull Request -
State: open - Opened by giovp over 1 year ago
- 2 comments
#416 - Expand to desired bounding box
Issue -
State: open - Opened by aeisenbarth over 1 year ago
#415 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: open - Opened by pre-commit-ci[bot] over 1 year ago
- 1 comment
#414 - Concatenating Multiple Spatialdata objects: Regions in the AnnData object and `cells_region` do not match.
Issue -
State: open - Opened by pakiessling over 1 year ago