Segment Anything for Microscopy

Tools for segmentation and tracking in microscopy build on top of Segment Anything. 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 using the tag micro-sam, and tagging @constantinpape and @anwai98. You can follow recent updates on micro_sam in our news feed.

Installation and Usage

Please check the documentation for details on how to install and use micro_sam. You can also watch the quickstart video, our virtual I2K workshop video or all video tutorials.

Contributing

We always welcome new contributions!

If you just want to suggest a documentation edit, you can do this directly here, on GitHub. For more complex changes, see CONTRIBUTING.md or the contributing guide in our documentation for details. The first step is to discuss your idea in a new issue with the current developers.

Everyone participating in this project is expected to follow our Code of Conduct.

Citation

If you are using this repository in your research please cite

• our paper (now published in Nature Methods!)
• and the original Segment Anything publication.
• If you use vit-tiny models please also cite Mobile SAM.
• If you use automatic tracking, please also cite Trackastra.
• If you use automatic prompt generation (APG), please also cite our APG paper.

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 and QuPath also offer integration of Segment Anything for interactive segmentation.

We have also built follow-up work that is based on micro_sam:

• https://github.com/computational-cell-analytics/patho-sam - improves SAM for histopathology.
• https://github.com/computational-cell-analytics/medico-sam - improves SAM for medical imaging.
• https://github.com/computational-cell-analytics/peft-sam - studies parameter efficient fine-tuning for SAM.

Release Overview

You can find an overview of changes introduced in previous releases here.