{"id":13716229,"url":"https://github.com/computational-cell-analytics/micro-sam","last_synced_at":"2025-05-07T05:32:36.934Z","repository":{"id":163404336,"uuid":"635751761","full_name":"computational-cell-analytics/micro-sam","owner":"computational-cell-analytics","description":"Segment Anything for Microscopy","archived":false,"fork":false,"pushed_at":"2025-05-04T17:52:57.000Z","size":54214,"stargazers_count":534,"open_issues_count":74,"forks_count":67,"subscribers_count":9,"default_branch":"master","last_synced_at":"2025-05-04T18:33:56.568Z","etag":null,"topics":["cell-segmentation","microscopy-images","mitochondria-segmentation","napari","nuclei-segmentation","segment-anything","segmentation"],"latest_commit_sha":null,"homepage":"https://computational-cell-analytics.github.io/micro-sam/","language":"Jupyter 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Notebook","funding_links":[],"categories":["Image processing and segmentation","🔬 Domain-Specific Applications"],"sub_categories":["🧬 Biology \u0026 Medicine"],"readme":"[![DOC](https://shields.mitmproxy.org/badge/docs-pdoc.dev-brightgreen.svg)](https://computational-cell-analytics.github.io/micro-sam/)\n[![Conda](https://anaconda.org/conda-forge/micro_sam/badges/version.svg)](https://anaconda.org/conda-forge/micro_sam)\n[![codecov](https://codecov.io/gh/computational-cell-analytics/micro-sam/graph/badge.svg?token=7ETPP5CABP)](https://codecov.io/gh/computational-cell-analytics/micro-sam)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7919746.svg)](https://doi.org/10.5281/zenodo.7919746)\n\n# Segment Anything for Microscopy\n\nTools for segmentation and tracking in microscopy build on top of [Segment Anything](https://segment-anything.com/).\nSegment and track objects in microscopy images interactively with a few clicks!\n\nWe implement napari applications for:\n- interactive 2d segmentation (Left: interactive cell segmentation)\n- interactive 3d segmentation (Middle: interactive mitochondria segmentation in EM)\n- interactive tracking of 2d image data (Right: interactive cell tracking)\n\n\u003cimg src=\"https://github.com/computational-cell-analytics/micro-sam/assets/4263537/d04cb158-9f5b-4460-98cd-023c4f19cccd\" width=\"256\"\u003e\n\u003cimg src=\"https://github.com/computational-cell-analytics/micro-sam/assets/4263537/dfca3d9b-dba5-440b-b0f9-72a0683ac410\" width=\"256\"\u003e\n\u003cimg src=\"https://github.com/computational-cell-analytics/micro-sam/assets/4263537/aefbf99f-e73a-4125-bb49-2e6592367a64\" width=\"256\"\u003e\n\nIf 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.\n\n\n## Installation and Usage\n\nPlease 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\u0026si=qNbB8IFXqAX33r_Z).\n\n\n## Contributing\n\nWe welcome new contributions!\n\nIf 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.\n\n\n## Citation\n\nIf you are using this repository in your research please cite\n- our [preprint](https://doi.org/10.1101/2023.08.21.554208)\n- and the original [Segment Anything publication](https://arxiv.org/abs/2304.02643).\n- If you use a `vit-tiny` models please also cite [Mobile SAM](https://arxiv.org/abs/2306.14289).\n\n\n## Related Projects\n\nThere are a few other napari plugins build around Segment Anything:\n- https://github.com/MIC-DKFZ/napari-sam (2d and 3d support)\n- https://github.com/royerlab/napari-segment-anything (only 2d support)\n- https://github.com/hiroalchem/napari-SAM4IS\n\nCompared to these we support more applications (2d, 3d and tracking), and provide finetuning methods and finetuned models for microscopy data.\n[WebKnossos](https://webknossos.org/) also offers integration of SegmentAnything for interactive segmentation.\n\n\n## Release Overview\n\n**New in version 1.0.1**\n\nUse stable URL for model downloads and fix issues in state precomputation for automatic segmentation.\n\n**New in version 1.0.0**\n\nThis release mainly fixes issues with the previous release and marks the napari user interface as stable.\n\n**New in version 0.5.0**\n\nThis version includes a lot of new functionality and improvements. The most important changes are:\n- Re-implementation of the annotation tools. The tools are now implemented as napari plugin.\n- Using our improved functionality for automatic instance segmentation in the annotation tools, including automatic segmentation for 3D data.\n- New widgets to use the finetuning and image series annotation functionality from napari.\n- Improved finetuned models for light microscopy and electron microscopy data that are available via bioimage.io.\n\n**New in version 0.4.1**\n\n- Bugfix for the image series annotator. Before the automatic segmentation did not work correctly.\n\n**New in version 0.4.0**\n\n- Significantly improved model finetuning\n- Update the finetuned models for microscopy, see [details in the doc](https://computational-cell-analytics.github.io/micro-sam/micro_sam.html#finetuned-models)\n- Training decoder for direct instance segmentation (not available via the GUI yet)\n- Refactored model download functionality using [pooch](https://pypi.org/project/pooch/)\n\n**New in version 0.3.0**\n\n- Support for ellipse and polygon prompts\n- Support for automatic segmentation in 3d\n- Training refactoring and speed-up of fine-tuning\n\n**New in version 0.2.1 and 0.2.2**\n\n- Several bugfixes for the newly introduced functionality in 0.2.0.\n\n**New in version 0.2.0**\n\n- Functionality for training / finetuning and evaluation of Segment Anything Models\n- Full support for our finetuned segment anything models\n- Improvements of the automated instance segmentation functionality in the 2d annotator\n- And several other small improvements\n\n**New in version 0.1.1**\n\n- Fine-tuned segment anything models for microscopy (experimental)\n- Simplified instance segmentation menu\n- Menu for clearing annotations\n\n**New in version 0.1.0**\n\n- We support tiling in all annotators to enable processing large images.\n- Implement new automatic instance segmentation functionality:\n    - That is faster.\n    - Enables interactive update of parameters.\n    - And also works for large images by making use of tiled embeddings.\n- Implement the `image_series_annotator` for processing many images in a row.\n- Use the data hash in pre-computed embeddings to warn if the input data changes.\n- Create a simple GUI to select which annotator to start.\n- And made many other small improvements and fixed bugs.\n\n**New in version 0.0.2**\n\n- We have added support for bounding box prompts, which provide better segmentation results than points in many cases.\n- Interactive tracking now uses a better heuristic to propagate masks across time, leading to better automatic tracking results.\n- And have fixed several small bugs.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcomputational-cell-analytics%2Fmicro-sam","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcomputational-cell-analytics%2Fmicro-sam","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcomputational-cell-analytics%2Fmicro-sam/lists"}