spatialdata-io

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API for reading in raw MCD files from IMC experiments

3

In the documentation for this package it states that Steinbock outputs from IMC image analysis can be read in through the API. I am wondering if there is a similar...

matt-sd-watson

Tasks: - [ ] modify the script on the new (updated) data available from the Spatial Genomics website - [ ] turn the `to_zarr.py` script from `spatialdata-sandbox` into a reader...

LucaMarconato

Using MultiValueEnum for MCMICRO

1

In some cases, there are multiple directories for which it contents needs to be parsed using a specific model. For example, the directory 'registration', 'dearray' and 'probability_maps' all contain images...

melonora

3D visualize

1

Hi developer. Thanks alot for the useful tools and sorry for keep bothering. I need a 3D visualiza on my xenium dataset. Now I can correctly load my xenium data...

Yifan-debug

Can't read re-segmented Xenium data

4

Hello, I have re-run cell segmentation for my Xenium data using Xenium Ranger version 2.0.0.12 to benefit from its improved segmentation algorithm. I can't read the re-segmented data with `spatialdata_io.xenium()`,...

liz-is

Xenium: use physical units instead of pixel units as references

6

Hi, I find the coordinate differs a lot between 10xXenium analyzer and spatialdata. This is figures from 10xXenium analyzer:  And this is from spatialdata (the same dataset as above,...

wangjiawen2013

Segmented CODEX data in QuPath csv to squidpy

1

Dear Community, I have stitched CODEX images directly after the run and I segemented the image in QuPath. The result is a csv where each row is a cell with...

andreevg04

Stereoseq expected directory structure

7

Hi Team, Would it be possible to document the expected directory structure for the `stereoseq` reader? The results we got from the stereoseq team don't follow the directory structure being...

aadimator

updates: - [github.com/psf/black: 24.4.2 → 24.8.0](https://github.com/psf/black/compare/24.4.2...24.8.0) - [github.com/pre-commit/mirrors-mypy: v1.11.0 → v1.11.2](https://github.com/pre-commit/mirrors-mypy/compare/v1.11.0...v1.11.2) - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v5.0.0) - [github.com/PyCQA/flake8: 7.1.0 → 7.1.1](https://github.com/PyCQA/flake8/compare/7.1.0...7.1.1) - [github.com/PyCQA/doc8: v1.1.1 → v1.1.2](https://github.com/PyCQA/doc8/compare/v1.1.1...v1.1.2)

pre-commit-ci[bot]

Polynucleated cells are sometimes detected in Xenium when using the Multimodal Segmentation Kit. The `xenium() XOA 2.0` reader has been developed on a preview version of the data which didn't...

LucaMarconato