spatialdata-io

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Confusion on constructing SpatialData object from the ground up

2

Hi, I am putting this in the `-io` package git page, but let me know if it's better to go in the general package page. I'm dealing with a set...

MiTPenguin

merscope reader remove invalid polygons

3

Reading invalid polygons causes the Merscope reader to fail. This should be rare, but I have run into this in one of our my datasets.

ckmah

Fix IO warning

2

Fixes ``` /home/lukas/miniforge3/envs/lamindb/lib/python3.12/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead. warnings.warn(msg, FutureWarning) ``` also modernizes the setup a tiny but and removes ancient flake8 and other stuff

Zethson

Chunkwise image loader

2

## Description This PR addresses the challenge that the currently implemented and planned image loaders require loading imaging data entirely into memory, typically as NumPy arrays. Given the large size...

lucas-diedrich

Fixes #298: Repeatedly appending parent path to flatFiles

1

**Purpose:** Fix for appending parent path to CSV file paths in `cosmx.py` reader module.

mayank-singh-sikarwar

New reader for G4X datasets (Singular Genomics)

4

👋 Hello @scverse/spatialdata and community, I would like to contribute the initial version of a `spatialdata-io` reader for Singular Genomics [G4X](https://singulargenomics.com/g4x/) datasets that I recently developed for internal use (I...

ckmah

New PR because [137](https://github.com/scverse/spatialdata-io/pull/137#issuecomment-2709837027) was too far behind `main`, while also not being up to date with Sopa.

quentinblampey

spatialdata_io.visium_hd() now allows users to select between 'raw_feature_bc_matrix.h5' and 'filtered_feature_bc_matrix.h5', but in the output of Space Ranger, there is also the 'raw_probe_bc_matrix.h5' file, which allows the analysis of counts on...

julienmortier

Hi spatialdata team, It seems that the parser function for cosmx data appends path to the file name two times: first, when checking whether the file exists, and second, [when...

tsvvas

updates: - [github.com/rbubley/mirrors-prettier: v3.5.1 → v3.5.3](https://github.com/rbubley/mirrors-prettier/compare/v3.5.1...v3.5.3) - [github.com/PyCQA/isort: 6.0.0 → 6.0.1](https://github.com/PyCQA/isort/compare/6.0.0...6.0.1) - [github.com/PyCQA/flake8: 7.1.2 → 7.2.0](https://github.com/PyCQA/flake8/compare/7.1.2...7.2.0)

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