steinbock

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Similar to https://github.com/VasylVaskivskyi/slice-stitch

jwindhager

updates: - [github.com/PyCQA/flake8: 7.0.0 → 7.1.0](https://github.com/PyCQA/flake8/compare/7.0.0...7.1.0) - [github.com/pre-commit/mirrors-mypy: v1.10.0 → v1.10.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.10.0...v1.10.1)

pre-commit-ci[bot]

Strange invalid literal error..

2

Hi I'm having a strange error, using code and an image which i've previously preprocessed before .. any advice would be really greatly appreciated. Commands I am using are as...

paulrbuckley-kcl

Different signal intensities for the same ROI

1

Hi, I performed the steinbock pipeline first with the mcd-file and then only with the txt-file for the same ROI. I figured out that the signal intensities (Folder: Steinbock/intensities/csv-file) are...

yasrod

updates: - [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/isort: 5.13.2 → 6.0.0](https://github.com/PyCQA/isort/compare/5.13.2...6.0.0) - [github.com/psf/black: 24.8.0 → 25.1.0](https://github.com/psf/black/compare/24.8.0...25.1.0) - [github.com/PyCQA/flake8: 7.1.1 → 7.1.2](https://github.com/PyCQA/flake8/compare/7.1.1...7.1.2) - [github.com/pre-commit/mirrors-mypy: v1.11.1 → v1.15.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.11.1...v1.15.0)

pre-commit-ci[bot]

Auto detect if `imwrite` should use ome and bigtiff or not

2

Related to: https://github.com/cgohlke/tifffile/issues/279 Recently, we have collaborators that report truncation of tifffiles written at the `steinbock preprocess imc images` step [here](https://github.com/BodenmillerGroup/steinbock/issues/271), presumably because of the ImageJ 4GB size limit. I...

matt-sd-watson

Hi I recently started to use steinbok in windows docker desktop but as soon as I run it, it automatically exits. and when I run the run it in the...

SamWell16

Set mask dtype to `np.uint32` by default without using ENV variables?

3

Previous discussion of how to specify unsigned 32-byte integer dtype for masks here: https://github.com/BodenmillerGroup/steinbock/issues/207 We have collaborators that are struggling with enforcing this env command when running steinbock either through...

matt-sd-watson

Command "preprocess imc images" generate tiff file with only image for one channel

1

Hi, I have been working with Steinbock for big IMC files ( more than 10G), one issue I am having now is the image preprocessing. It generated a tiff file...

xwxdazhong