Develop #218
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…teinbock into milad_develop
updates: - [github.com/PyCQA/autoflake: v2.0.1 → v2.0.2](PyCQA/autoflake@v2.0.1...v2.0.2) - [github.com/psf/black: 23.1.0 → 23.3.0](psf/black@23.1.0...23.3.0) - [github.com/pre-commit/mirrors-mypy: v1.0.0 → v1.2.0](pre-commit/mirrors-mypy@v1.0.0...v1.2.0)
…nfig [pre-commit.ci] pre-commit autoupdate
for more information, see https://pre-commit.ci
…cellpose implementation
…teinbock into milad_develop
for more information, see https://pre-commit.ci
…teinbock into milad_develop
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
…teinbock into milad_develop
for more information, see https://pre-commit.ci
…teinbock into milad_develop
for more information, see https://pre-commit.ci
updates: - [github.com/PyCQA/autoflake: v2.0.2 → v2.2.0](PyCQA/autoflake@v2.0.2...v2.2.0) - [github.com/psf/black: 23.3.0 → 23.7.0](psf/black@23.3.0...23.7.0) - [github.com/PyCQA/flake8: 6.0.0 → 6.1.0](PyCQA/flake8@6.0.0...6.1.0) - [github.com/pre-commit/mirrors-mypy: v1.2.0 → v1.5.1](pre-commit/mirrors-mypy@v1.2.0...v1.5.1)
update develop with recent changes in main (bug fixes etc)
… into cellpose_app
Cellpose app
Co-authored-by: Jonas Windhager <[email protected]>
Co-authored-by: Jonas Windhager <[email protected]>
for more information, see https://pre-commit.ci
Co-authored-by: Jonas Windhager <[email protected]>
for more information, see https://pre-commit.ci
Update readimc to 0.7.0 + lenient parsing option
removed the --rebase parameter of mike is not supported.
…nfig [pre-commit.ci] pre-commit autoupdate
Update build.yml
standard runners cannot build steinbock-cellpose, switching to larger runners.
for more information, see https://pre-commit.ci
Update build.yml to use self-hosted runner
updates: - [github.com/psf/black: 24.4.2 → 24.8.0](psf/black@24.4.2...24.8.0) - [github.com/PyCQA/flake8: 7.0.0 → 7.1.1](PyCQA/flake8@7.0.0...7.1.1) - [github.com/pre-commit/mirrors-mypy: v1.10.0 → v1.11.1](pre-commit/mirrors-mypy@v1.10.0...v1.11.1)
…nfig [pre-commit.ci] pre-commit autoupdate
for more information, see https://pre-commit.ci
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Cellposeadded as an app (steinbock/_cli/apps.py).Cellposemodel training added (steinbock/segmentation/_cli/train.py', 'steinbock/segmentation/train.py, 'Steinbock/segmentation/_cli/_cli.py').Cellposedefault parameters changed (steinbock/segmentation/cellpose.py).Cellposemodel zoo added (steinbock/segmentation/_cli/cellpose.py).CONTRIBUTORS.md).CHANGELOG.mdupdated.docs/cli/segmentation.md).docs/cli/utils.md).docs/install-docker.md).Opencv-python==4.8.0.74added to requirements, it was needed to run cellpose training (requirements.txt).steinbock/preprocessing/imc.py).