{"id":19215822,"url":"https://github.com/vanvalenlab/cellsam","last_synced_at":"2025-04-07T15:06:25.248Z","repository":{"id":222566149,"uuid":"757751896","full_name":"vanvalenlab/cellSAM","owner":"vanvalenlab","description":"Codebase for \"A Foundation Model for Cell Segmentation\"","archived":false,"fork":false,"pushed_at":"2025-03-26T21:26:53.000Z","size":16155,"stargazers_count":74,"open_issues_count":23,"forks_count":12,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-31T14:11:32.475Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vanvalenlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-02-14T22:41:18.000Z","updated_at":"2025-03-28T10:22:06.000Z","dependencies_parsed_at":"2024-02-15T00:30:30.153Z","dependency_job_id":"7f7bd93c-99ba-40ea-8d26-e7b0d5a4d164","html_url":"https://github.com/vanvalenlab/cellSAM","commit_stats":null,"previous_names":["vanvalenlab/cellsam"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vanvalenlab%2FcellSAM","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vanvalenlab%2FcellSAM/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vanvalenlab%2FcellSAM/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vanvalenlab%2FcellSAM/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vanvalenlab","download_url":"https://codeload.github.com/vanvalenlab/cellSAM/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247675596,"owners_count":20977376,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-09T14:14:55.795Z","updated_at":"2025-04-07T15:06:25.159Z","avatar_url":"https://github.com/vanvalenlab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CellSAM: A Foundation Model for Cell Segmentation\n\n[  \u003cimg src=\"https://github.com/rdilip/cellsam_inference/assets/9993319/1f40b5a5-60f1-4980-997d-6059e20d6133\" alt=\"Try the demo!\" style=\"width: 100%;\"\u003e\n](https://cellsam.deepcell.org/)\n\n## Description\nThis repository provides inference code for CellSAM. CellSAM is described in more detail in the [preprint](https://www.biorxiv.org/content/10.1101/2023.11.17.567630v3), and is publicly deployed at [cellsam.deepcell.org](https://cellsam.deepcell.org/). CellSAM achieves state-of-the-art performance on segmentation across a variety of cellular targets (bacteria, tissue, yeast, cell culture, etc.) and imaging modalities (brightfield, fluorescence, phase, etc.). Feel free to [reach out](mailto:ulisrael@caltech.edu) for support/questions! The full dataset used to train CellSAM is available [here](https://storage.googleapis.com/cellsam-data/dataset.tar.gz). This dataset contains cellpose data which is subject to the cellpose license [here](https://github.com/mouseland/cellpose?tab=BSD-3-Clause-1-ov-file). The cellpose data can also be downloaded from [here](https://www.cellpose.org/dataset).\n\n## Getting started\nThe easiest way to get started with CellSAM is with pip\n`pip install git+https://github.com/vanvalenlab/cellSAM.git`\n\nCellSAM requires `python\u003e=3.10`, but otherwise uses pure PyTorch. A sample image is included in this repository. Segmentation can be performed as follows\n\n```\nimport numpy as np\nfrom cellSAM import segment_cellular_image\nimg = np.load(\"sample_imgs/yeaz.npy\")\nmask, _, _ = segment_cellular_image(img, device='cuda')\n```\n\nFor more details, see `cellsam_introduction.ipynb`.\n\n### Napari package\nCellSAM includes a basic napari package for annotation functionality. To install the additional napari dependencies, use pip.\n\n`pip install git+https://github.com/vanvalenlab/cellSAM.git#egg=cellsam[napari]`\n\nTo launch the napari app, run `cellsam napari`. \n\n## Citation\n\nPlease cite us if you use CellSAM.\n\n```\n@article{israel2023foundation,\n  title={A Foundation Model for Cell Segmentation},\n  author={Israel, Uriah and Marks, Markus and Dilip, Rohit and Li, Qilin and Schwartz, Morgan and Pradhan, Elora and Pao, Edward and Li, Shenyi and Pearson-Goulart, Alexander and Perona, Pietro and others},\n  journal={bioRxiv},\n  publisher={Cold Spring Harbor Laboratory Preprints},\n  doi = {10.1101/2023.11.17.567630},\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvanvalenlab%2Fcellsam","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvanvalenlab%2Fcellsam","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvanvalenlab%2Fcellsam/lists"}