Cellpose

Latest version: v3.1.1.1

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3.1.1

New distributed cellpose module enables running of cellpose on really big data, on workstations and clusters, thanks to the heroic work of GFleishman ! Check out the documentation [here](https://cellpose.readthedocs.io/en/latest/distributed.html).

We made bug fixes for Mac from v3.1 and other small bug fixes, thanks to all the contributors.

What's Changed
* fix bug with channels=None in CellposeDenoiseModel (1098)
* add z_axis in CellposeDenoiseModel (1099)
* to avoid MPS errors, use CPU for Mac in `get_masks_torch` and use float32 in `_extend_centers_gpu` (1034, 1063, 1097)
* fix now masks found issue (1038)
* add weights_only flag (1042)
* bug with invert=True (1056)
* fix issue with version splitting (1074)
* fix bug with anisotropy in make_train (1076)
* fixing issue when channels and z are equal in stack (1086)
* Larger than memory images: performant and scalable distributed implementation for workstations and clusters by GFleishman in https://github.com/MouseLand/cellpose/pull/1062
* Bugfix: Removing unused 'ARBITRARY_SIZE' by Pablo1990 in https://github.com/MouseLand/cellpose/pull/1082
* train.py: remove superfluous percent sign in f-string by deroulers in https://github.com/MouseLand/cellpose/pull/1077
* Add norm percentiles as CLI argument by TheBestDestroyer in https://github.com/MouseLand/cellpose/pull/1058
* [Doc] Describe how to manage multithreading by royjacobson in https://github.com/MouseLand/cellpose/pull/1045
* Fix saving of flow fields and cell probability in GUI by qin-yu in https://github.com/MouseLand/cellpose/pull/1103
* File selection cancel logic added by knowblesse in https://github.com/MouseLand/cellpose/pull/1040
* feat: custom output name by antoinemeyer5 in https://github.com/MouseLand/cellpose/pull/1104

New Contributors
* GFleishman made their first contribution in https://github.com/MouseLand/cellpose/pull/1062
* Pablo1990 made their first contribution in https://github.com/MouseLand/cellpose/pull/1082
* deroulers made their first contribution in https://github.com/MouseLand/cellpose/pull/1077
* TheBestDestroyer made their first contribution in https://github.com/MouseLand/cellpose/pull/1058
* royjacobson made their first contribution in https://github.com/MouseLand/cellpose/pull/1045
* knowblesse made their first contribution in https://github.com/MouseLand/cellpose/pull/1040
* antoinemeyer5 made their first contribution in https://github.com/MouseLand/cellpose/pull/1104

**Full Changelog**: https://github.com/MouseLand/cellpose/compare/v3.1.0...v3.1.1

3.1.0

Check out the additional options for performing 3D segmenation, and more guidance [here](https://cellpose.readthedocs.io/en/latest/do3d.html). Also, the latest mask creation function `get_masks_torch` reduces CPU RAM usage compared to the previous version, and is available to run on the GPU for faster mask creation.

Updated info with CPU/GPU RAM usage and approx runtimes for single images, available [here](https://cellpose.readthedocs.io/en/latest/benchmark.html).

Also we should have full compatibility with MPS at least in 2D (thanks OratHelm !) And thanks to qin-yu you can share your cellpose models to the bioimage.io model zoo.

What's Changed
* MPS compatibility on Apple Silicon by OratHelm in https://github.com/MouseLand/cellpose/pull/1003
* Rev3 by carsen-stringer, adds additional denoising models and anisotropy models, in https://github.com/MouseLand/cellpose/pull/1008
* Add missing train/test files to _process_train_test() call by kemaleren in https://github.com/MouseLand/cellpose/pull/995
* `imagecodecs` no longer compiles with `python 3.8` by ajinkya-kulkarni in https://github.com/MouseLand/cellpose/pull/979
* Fix link in doc by maweigert in https://github.com/MouseLand/cellpose/pull/970
* allows --all channels to work in CLI by lacan in https://github.com/MouseLand/cellpose/pull/949
* Export CPnet to BioImage.IO Model Zoo by qin-yu in https://github.com/MouseLand/cellpose/pull/988
* Bugfix: Resizing masks containing over 65,535 cells not supported by OpenCV by Tobiaspk in https://github.com/MouseLand/cellpose/pull/938
* Add .flex to the allowed image file extensions by mmasinas in https://github.com/MouseLand/cellpose/pull/881
* added optional params cp_path and logfile_name to the setup_logger fu… by MaxJoas in https://github.com/MouseLand/cellpose/pull/862
* Skip empty outlines and display a message in the console. by francodgstn in https://github.com/MouseLand/cellpose/pull/829
* Fix intensity normalizations by qin-yu in https://github.com/MouseLand/cellpose/pull/981
* Add docs for BioImage.IO: finding & sharing models by qin-yu in https://github.com/MouseLand/cellpose/pull/1011
* New3d by carsen-stringer, adds new mask creation script on GPU, in https://github.com/MouseLand/cellpose/pull/1030
* GUI selection for SGD/RAdam Training by ian-coccimiglio in https://github.com/MouseLand/cellpose/pull/1022

New Contributors
* OratHelm made their first contribution in https://github.com/MouseLand/cellpose/pull/1003
* kemaleren made their first contribution in https://github.com/MouseLand/cellpose/pull/995
* maweigert made their first contribution in https://github.com/MouseLand/cellpose/pull/970
* lacan made their first contribution in https://github.com/MouseLand/cellpose/pull/949
* qin-yu made their first contribution in https://github.com/MouseLand/cellpose/pull/988
* Tobiaspk made their first contribution in https://github.com/MouseLand/cellpose/pull/938
* mmasinas made their first contribution in https://github.com/MouseLand/cellpose/pull/881
* MaxJoas made their first contribution in https://github.com/MouseLand/cellpose/pull/862
* ian-coccimiglio made their first contribution in https://github.com/MouseLand/cellpose/pull/1022

**Full Changelog**: https://github.com/MouseLand/cellpose/compare/v3.0.10...v3.1.0

3.0.10

* fix bug in diameter changing when rerunning the model after training -- should make Cellpose 3 training parameters now equivalent to Cellpose 2
* fix bug with nimg_per_epoch being fixed to 8 when training in the GUI (925)

3.0.8

- Update install instructions to include `venv`
- Documentation fixes and additions
- Small bug fixes
- fix `io.masks_flows_to_seg()` iteration bug

3.0.5

Cellpose3 release with CLI, API and GUI support! Check out docs for updates to code: https://cellpose.readthedocs.io/en/latest/restore.html

3.0.1

first Cellpose 3 release!

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