v4.0.4

Introducing Cellpose-SAM!

New in cellpose v4

• Cellpose-SAM aka CP4 is fully integrated in to the CLI/API/GUI and notebooks
• cellpose.models.Cellpose class was removed, users should now only use cellpose.models.CellposeModel
• Size estimation via cellpose.models.SizeModel class was removed. Users don't have to use the diameter setting since CP4 is much more robust to object size.
• Denoising components via cellpose.denoise is currently not available.
• Added more comprehensive testing
• Better utilization of MPS for Mac users when doing 3D segmentation
• Added --save_each flag for training from the CLI
• More details are available in the paper, talk, and in the docs.

New Contributors

• @KevinCortacero made their first contribution in #1080
• @unikill066 made their first contribution in #1159

Changelog for early cellpose v4 changes: v4.0.1...v4.0.4

v3.1.1.2

This is the last release of Cellpose3 before the Cellpose-SAM release.

What's Changed

• fix tiling bug when augment=True
• Documented using masks and preprocessing_steps in distributed rst by @GFleishman in #1108
• Compress TIFFs on save by @qin-yu in #1131
• Report errors when saving masks to *_seg.npy by @deroulers in #1129
• Correct GUI initialization order of load_3D for modular usage. by @biswajitSM in #1119
• Optimize fill_holes_and_remove_small_masks by @Tomvl117 in #1116
• pyarrow missing by @GFleishman in #1109

New Contributors

• @biswajitSM made their first contribution in #1119
• @Tomvl117 made their first contribution in #1116

Full Changelog: v3.1.1.1...v3.1.1.2

v3.1.1

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.

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 #1062
• Bugfix: Removing unused 'ARBITRARY_SIZE' by @Pablo1990 in #1082
• train.py: remove superfluous percent sign in f-string by @deroulers in #1077
• Add norm percentiles as CLI argument by @TheBestDestroyer in #1058
• [Doc] Describe how to manage multithreading by @royjacobson in #1045
• Fix saving of flow fields and cell probability in GUI by @qin-yu in #1103
• File selection cancel logic added by @knowblesse in #1040
• feat: custom output name by @antoinemeyer5 in #1104

New Contributors

• @GFleishman made their first contribution in #1062
• @Pablo1990 made their first contribution in #1082
• @deroulers made their first contribution in #1077
• @TheBestDestroyer made their first contribution in #1058
• @royjacobson made their first contribution in #1045
• @knowblesse made their first contribution in #1040
• @antoinemeyer5 made their first contribution in #1104

Full Changelog: v3.1.0...v3.1.1

v3.1.0

Check out the additional options for performing 3D segmenation, and more guidance here. 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.

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

New Contributors

• @OratHelm made their first contribution in #1003
• @kemaleren made their first contribution in #995
• @maweigert made their first contribution in #970
• @lacan made their first contribution in #949
• @qin-yu made their first contribution in #988
• @Tobiaspk made their first contribution in #938
• @mmasinas made their first contribution in #881
• @MaxJoas made their first contribution in #862
• @ian-coccimiglio made their first contribution in #1022

Full Changelog: v3.0.10...v3.1.0

Cellpose v3.0.10

• 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)

Cellpose v3.0.8

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

Cellpose v3.0.5

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

Cellpose v3.0.1

first Cellpose 3 release!

cellpose v2.3.2

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)

cellpose v2.2.2

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