{"name":"micro_sam","display_name":"Segment Anything for Microscopy","visibility":"public","icon":"","categories":["Segmentation","Annotation"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"micro_sam.sample_data_wholeslide","title":"Load WholeSlide sample data from micro_sam plugin","python_name":"micro_sam.sample_data:sample_data_wholeslide","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"micro_sam.sample_data_livecell","title":"Load LiveCell sample data from micro_sam plugin","python_name":"micro_sam.sample_data:sample_data_livecell","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"micro_sam.sample_data_hela_2d","title":"Load 2D Hela sample data from micro_sam plugin","python_name":"micro_sam.sample_data:sample_data_hela_2d","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"micro_sam.sample_data_3d","title":"Load Lucchi++ 3D sample data from micro_sam 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Classifier","autogenerate":false},{"command":"micro_sam.training","display_name":"Finetuning","autogenerate":false},{"command":"micro_sam.settings","display_name":"Settings","autogenerate":false}],"sample_data":[{"command":"micro_sam.sample_data_wholeslide","key":"micro_sam-wholeslide","display_name":"WholeSlide example data"},{"command":"micro_sam.sample_data_livecell","key":"micro_sam-livecell","display_name":"LiveCell 2d example data"},{"command":"micro_sam.sample_data_hela_2d","key":"micro_sam-hela2d","display_name":"HeLa 2d example data"},{"command":"micro_sam.sample_data_3d","key":"micro_sam-lucchi","display_name":"Lucchi++ 3d dataset"},{"command":"micro_sam.sample_data_tracking","key":"micro_sam-tracking","display_name":"Tracking sample dataset"},{"command":"micro_sam.sample_data_segmentation","key":"micro_sam-segmentation","display_name":"Segmentation sample dataset"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"micro_sam","version":"1.8.2","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Segment Anything For Microscopy","description":"[![DOC](https://shields.mitmproxy.org/badge/docs-pdoc.dev-brightgreen.svg)](https://computational-cell-analytics.github.io/micro-sam/)\n[![PyPI](https://img.shields.io/pypi/v/micro_sam.svg)](https://pypi.org/project/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\n\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\n\n\n\nIf you run into any problems or have questions regarding our tool please open an [issue](https://github.com/computational-cell-analytics/micro-sam/issues/new/choose) on Github or reach out via [image.sc](https://forum.image.sc/) using the tag `micro-sam`, and tagging [@constantinpape](https://forum.image.sc/u/constantinpape/summary) and [@anwai98](https://forum.image.sc/u/anwai98/summary).\nYou can follow recent updates on `micro_sam` in our [news feed](https://forum.image.sc/t/microsam-news-feed).\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), [our virtual I2K workshop video](https://www.youtube.com/watch?v=dxjU4W7bCis&list=PLdA9Vgd1gxTbvxmtk9CASftUOl_XItjDN&index=33) or [all video tutorials](https://youtube.com/playlist?list=PLwYZXQJ3f36GQPpKCrSbHjGiH39X4XjSO&si=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 [paper](https://www.nature.com/articles/s41592-024-02580-4) (now published in Nature Methods!)\n- and the original [Segment Anything publication](https://arxiv.org/abs/2304.02643).\n- If you use `vit-tiny` models please also cite [Mobile SAM](https://arxiv.org/abs/2306.14289).\n- If you use automatic tracking, please also cite [Trackastra](https://arxiv.org/abs/2405.15700).\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/) and [QuPath](https://qupath.github.io/) also offer integration of Segment Anything for interactive segmentation.\n\nWe have also built follow-up work that is based on `micro_sam`:\n- https://github.com/computational-cell-analytics/patho-sam - improves SAM for histopathology.\n- https://github.com/computational-cell-analytics/medico-sam - improves SAM for medical imaging.\n- https://github.com/computational-cell-analytics/peft-sam - studies parameter efficient fine-tuning for SAM.\n\n## Release Overview\n\nYou can find an overview of changes introduced in previous releases [here](https://github.com/computational-cell-analytics/micro-sam/blob/main/RELEASE_OVERVIEW.md).\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/computational-cell-analytics/micro-sam","download_url":null,"author":"Anwai Archit, Paul Hilt, Genevieve Buckley, Constantin Pape","author_email":null,"maintainer":null,"maintainer_email":null,"license":"MIT","classifier":["Development Status :: 5 - Production/Stable","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: MIT License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Programming Language :: Python :: 3.14","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["bioimage-cpp>=0.3","bioimageio.core","h5py","imagecodecs","imageio","joblib","kornia","magicgui","matplotlib","napari<0.7","natsort","networkx","numpy","pandas","pooch","PyQt5","python-elf>=0.9","scikit-image","scikit-learn","segment-anything","superqt","timm","torch>=2.5","torch-em>=0.9","torchvision","tqdm","trackastra>=0.5.3","xarray","xxhash","zarr"],"requires_python":">=3.10","requires_external":null,"project_url":["Bug Tracker, https://github.com/computational-cell-analytics/micro-sam/issues","Documentation, https://computational-cell-analytics.github.io/micro-sam/micro_sam.html","Source Code, https://github.com/computational-cell-analytics/micro-sam","User Support, https://github.com/computational-cell-analytics/micro-sam/issues"],"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}