Cellpose

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

first Cellpose 3 release!

Last release of Cellpose 2 before update to Cellpose 3.

- fix slow stitching problem by only checking ROIs for stitching in current plane (issue 845)
- fix reshaping issue in flows from mrariden ('mrariden-dynamics_reshape_fix' )
- add python 3.11 support from harryzcy (807)
- disable multiproc on windows from mrariden
- fixes bug in 3D interpolation for multi-ROI masks
- disable gui autosave from mrariden (784)
- fix min size from SimonBon (781)
- fix imagej_roi_converter from francodgstn (828)
- fix torch version command (831)
- fix zaxis=0 bug from nickeener (688)
- add a pyqt version to env from rhoadesScholar (849)
- fix for multimodel adding to gui from landoskape (839)

Changes added to main branch
- Added functionality to allow saving ROIs in ImageJ-native format.
- Minor bug fix related to saving images with many objects thanks to alix-simon
- Performance improvement using improved indexing thanks to sophiamaedler
- Update Read the Docs to include a FAQ section, and misc RTD updates
- Add multithreading to 'outlines' exporting to speed up saving/execution time

* fixing deprecation of `np.bool`
* mrariden improved docs, added auto compilation of CLI page
* FrickTobias fixed a bug for memory info (647 )
* fixed version checking for torch 2.0 release

Implementing some minor fixes and updates
* cellpose passes tests for python 3.9 and 3.10 across operating systems -- we still recommend python 3.8, particularly if you have issues with the install
* added option to use Mac M1 chip (if installed with torch) with command line argument `--gpu device mps`
* added option to run cellpose on a single file from the command like with `--image_path` as an alternative to `--dir` (543)
* added new suggestion mode to suggest best Cellpose 2 model
* suppressed writing PNGs or outlines when no masks were found (584)
* added docs for all functions (554)
* fixed case sensitive image file detection (555)
* allow `eval` method of `Cellpose` and `CellposeModel` to take as input torch arrays (557)
* added the function `io.add_model(/full/path/to/model)` to add the model file to the hidden folder to use with GUI and CLI; can also access the function by running `python -m cellpose --add_model /full/path/to/model` (558)
* fixed issue with cursor not allowing resizing (545 )
* added mac instructions (523)
* forced tiff saving for masks > 2**16 (524)
* added pyqt5 import statement for windows 8.1 compatibility