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scverse/spatialdata-io: v0.7.0

Authors: LucaMarconato; Calogero Carlino; Wouter-Michiel Vierdag; LLehner; Giovanni Palla; Quentin Blampey; Lucas Diedrich; +22 Authors

scverse/spatialdata-io: v0.7.0

Abstract

<!-- Release notes generated using configuration in .github/release.yml at main --> What's Changed Added Add spatialdata-io version and reader name to attrs by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/360 Allow overriding scale_factor in visium hd by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/394 Changed Xenium: cache zip store opening; vectorize cell id encoding by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/370 Faster imports by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/373 Improve Xenium performance, fix multinucleate cells bug by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/376 Refactor xenium reader by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/386 feat: add support for non-gex data in visium hd by @stephenwilliams22 in https://github.com/scverse/spatialdata-io/pull/391 Use scanpy for reading matrixes by @cgeyskens in https://github.com/scverse/spatialdata-io/pull/292 Fixed Faster xenium points parsing by precomputing categories by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/363 Faster xenium polygon parsing via ragged arrays by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/365 Xenium avoid calling get_element_instances(); fix deprecation warning by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/369 fix codex reader - table by @nilchia in https://github.com/scverse/spatialdata-io/pull/377 fix visium_hd reader by @Mira-Kreuzer in https://github.com/scverse/spatialdata-io/pull/389 Fixes #298: Repeatedly appending parent path to flatFiles by @mayank-singh-sikarwar in https://github.com/scverse/spatialdata-io/pull/305 adjusted docstrings in steinbock reader py file by @LukasHats in https://github.com/scverse/spatialdata-io/pull/165 Handle autofluorescence channels and pass through unknown image types by @MSHelm in https://github.com/scverse/spatialdata-io/pull/368 Align CLI arguments with reader APIs for full parameter consistency by @Copilot in https://github.com/scverse/spatialdata-io/pull/321 New Contributors @nilchia made their first contribution in https://github.com/scverse/spatialdata-io/pull/377 @Mira-Kreuzer made their first contribution in https://github.com/scverse/spatialdata-io/pull/389 @mayank-singh-sikarwar made their first contribution in https://github.com/scverse/spatialdata-io/pull/305 @LukasHats made their first contribution in https://github.com/scverse/spatialdata-io/pull/165 @cgeyskens made their first contribution in https://github.com/scverse/spatialdata-io/pull/292 @Copilot made their first contribution in https://github.com/scverse/spatialdata-io/pull/321 Full Changelog: https://github.com/scverse/spatialdata-io/compare/v0.6.0...v0.7.0

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