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https://github.com/computational-cell-analytics/micro-sam

Segment Anything for Microscopy
https://github.com/computational-cell-analytics/micro-sam

cell-segmentation microscopy-images mitochondria-segmentation napari nuclei-segmentation segment-anything segmentation

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Segment Anything for Microscopy

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# Segment Anything for Microscopy



Tools for segmentation and tracking in microscopy build on top of [Segment Anything](https://segment-anything.com/).

Segment and track objects in microscopy images interactively with a few clicks!



We implement napari applications for:

- interactive 2d segmentation (Left: interactive cell segmentation)

- interactive 3d segmentation (Middle: interactive mitochondria segmentation in EM)

- interactive tracking of 2d image data (Right: interactive cell tracking)










If you run into any problems or have questions regarding our tool please open an issue on Github or reach out via [image.sc](https://forum.image.sc/) using the tag `micro-sam` and tagging @constantinpape.



## Installation and Usage



Please check [the documentation](https://computational-cell-analytics.github.io/micro-sam/) for details on how to install and use `micro_sam`. You can also watch [the quickstart video](https://youtu.be/gcv0fa84mCc) or [all video tutorials](https://youtube.com/playlist?list=PLwYZXQJ3f36GQPpKCrSbHjGiH39X4XjSO&si=qNbB8IFXqAX33r_Z).



## Contributing



We welcome new contributions!



If you are interested in contributing to micro-sam, please see the [contributing guide](https://computational-cell-analytics.github.io/micro-sam/micro_sam.html#contribution-guide). The first step is to [discuss your idea in a new issue](https://github.com/computational-cell-analytics/micro-sam/issues/new) with the current developers.



## Citation



If you are using this repository in your research please cite

- our [preprint](https://doi.org/10.1101/2023.08.21.554208)

- and the original [Segment Anything publication](https://arxiv.org/abs/2304.02643).

- If you use a `vit-tiny` models please also cite [Mobile SAM](https://arxiv.org/abs/2306.14289).



## Related Projects



There are a few other napari plugins build around Segment Anything:

- https://github.com/MIC-DKFZ/napari-sam (2d and 3d support)

- https://github.com/royerlab/napari-segment-anything (only 2d support)

- https://github.com/hiroalchem/napari-SAM4IS



Compared to these we support more applications (2d, 3d and tracking), and provide finetuning methods and finetuned models for microscopy data.

[WebKnossos](https://webknossos.org/) also offers integration of SegmentAnything for interactive segmentation.



## Release Overview



**New in version 1.0.1**



Use stable URL for model downloads and fix issues in state precomputation for automatic segmentation.



**New in version 1.0.0**



This release mainly fixes issues with the previous release and marks the napari user interface as stable.



**New in version 0.5.0**



This version includes a lot of new functionality and improvements. The most important changes are:

- Re-implementation of the annotation tools. The tools are now implemented as napari plugin.

- Using our improved functionality for automatic instance segmentation in the annotation tools, including automatic segmentation for 3D data.

- New widgets to use the finetuning and image series annotation functionality from napari.

- Improved finetuned models for light microscopy and electron microscopy data that are available via bioimage.io.



**New in version 0.4.1**



- Bugfix for the image series annotator. Before the automatic segmentation did not work correctly.



**New in version 0.4.0**



- Significantly improved model finetuning

- Update the finetuned models for microscopy, see [details in the doc](https://computational-cell-analytics.github.io/micro-sam/micro_sam.html#finetuned-models)

- Training decoder for direct instance segmentation (not available via the GUI yet)

- Refactored model download functionality using [pooch](https://pypi.org/project/pooch/)



**New in version 0.3.0**



- Support for ellipse and polygon prompts

- Support for automatic segmentation in 3d

- Training refactoring and speed-up of fine-tuning



**New in version 0.2.1 and 0.2.2**



- Several bugfixes for the newly introduced functionality in 0.2.0.



**New in version 0.2.0**



- Functionality for training / finetuning and evaluation of Segment Anything Models

- Full support for our finetuned segment anything models

- Improvements of the automated instance segmentation functionality in the 2d annotator

- And several other small improvements



**New in version 0.1.1**



- Fine-tuned segment anything models for microscopy (experimental)

- Simplified instance segmentation menu

- Menu for clearing annotations



**New in version 0.1.0**



- We support tiling in all annotators to enable processing large images.

- Implement new automatic instance segmentation functionality:

    - That is faster.

    - Enables interactive update of parameters.

    - And also works for large images by making use of tiled embeddings.

- Implement the `image_series_annotator` for processing many images in a row.

- Use the data hash in pre-computed embeddings to warn if the input data changes.

- Create a simple GUI to select which annotator to start.

- And made many other small improvements and fixed bugs.



**New in version 0.0.2**



- We have added support for bounding box prompts, which provide better segmentation results than points in many cases.

- Interactive tracking now uses a better heuristic to propagate masks across time, leading to better automatic tracking results.

- And have fixed several small bugs.