{"id":24619287,"url":"https://github.com/computational-cell-analytics/medico-sam","last_synced_at":"2025-10-06T10:32:27.630Z","repository":{"id":273663002,"uuid":"808646787","full_name":"computational-cell-analytics/medico-sam","owner":"computational-cell-analytics","description":"Segment Anything for Medical Imaging","archived":false,"fork":false,"pushed_at":"2025-01-22T07:50:01.000Z","size":223,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-22T08:32:51.742Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/computational-cell-analytics.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2024-05-31T14:03:01.000Z","updated_at":"2025-01-22T07:50:04.000Z","dependencies_parsed_at":"2025-01-22T08:33:01.255Z","dependency_job_id":"3c42a78a-3e37-4f08-b288-b9df431f3ad4","html_url":"https://github.com/computational-cell-analytics/medico-sam","commit_stats":null,"previous_names":["computational-cell-analytics/medico-sam"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/computational-cell-analytics%2Fmedico-sam","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/computational-cell-analytics%2Fmedico-sam/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/computational-cell-analytics%2Fmedico-sam/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/computational-cell-analytics%2Fmedico-sam/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/computational-cell-analytics","download_url":"https://codeload.github.com/computational-cell-analytics/medico-sam/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":235519884,"owners_count":19003201,"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":"2025-01-25T00:02:36.188Z","updated_at":"2025-10-06T10:32:27.617Z","avatar_url":"https://github.com/computational-cell-analytics.png","language":"Python","funding_links":[],"categories":["Paper List"],"sub_categories":["Follow-up Papers"],"readme":"# MedicoSAM: Towards foundation models for medical image segmentation\n\n\u003ca href=\"https://github.com/computational-cell-analytics/medico-sam\"\u003e\u003cimg src=\"https://github.com/computational-cell-analytics/medico-sam/blob/master/docs/logos/logo.png\" width=\"200\" align=\"right\"\u003e\n\nMedicoSAM implements interactive annotation and (automatic) semantic segmentation for medical images. It is built on top of [Segment Anything](https://segment-anything.com/) by Meta AI and specializes it for biomedical imaging data. Its core components are:\n- The `medico_sam` publicly available model for interactive data annotation in 2d and 3d data that are fine-tuned on publicly available medical images.\n- The `medico_sam` library provides training frameworks, inspired by [Segment Anything for Microscopy](https://computational-cell-analytics.github.io/micro-sam/micro_sam.html), for downstream tasks:\n  - Apply Segment Anything to 2d and 3d data or fine-tune it on your data.\n  - Supports semantic segmentation for 2d and 3d data, featuring an additional pretrained segmentation decoder.\n\nBased on these components, `medico_sam` enables fast interactive and automatic annotation for medical images.\n\n## Installation\n\nHow to install `medico-sam` python library from source?\n\nTo create the environment and install `medico_sam` into it follow these steps:\n\n1. Clone the repository: `git clone https://github.com/computational-cell-analytics/medico-sam`\n2. Enter it: `cd medico-sam`\n3. Create the environment with the necessary requirements: `conda env create -f environment.yaml`\n4. Activate the environment: `conda activate medico-sam`\n5. Install `medico_sam`: `pip install -e .`\n\n## Download Model Checkpoints\n\nYou can find the model checkpoints at: https://owncloud.gwdg.de/index.php/s/f5Ol4FrjPQWfjUF\n\nDownload it via terminal using: `wget https://owncloud.gwdg.de/index.php/s/f5Ol4FrjPQWfjUF/download -O vit_b_medicosam.pt`.\n\n## Tool Usage for Interactive Annotation\n\nSee [`TOOL_USAGE.md`](./TOOL_USAGE.md) document for details.\n\n\u003e TLDR: We recommend using our model with [`micro-sam`](https://github.com/computational-cell-analytics/micro-sam) annotator tool, in terms of compatibility and ease of annotation experience!\n\n## Citation\nIf you are using this repository in your research please cite:\n\n- our [preprint](https://doi.org/10.48550/arXiv.2501.11734).\n- the [Segment Anything fo Microscopy](https://www.nature.com/articles/s41592-024-02580-4) publication.\n- and the original [Segment Anything](https://arxiv.org/abs/2304.02643) publication.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcomputational-cell-analytics%2Fmedico-sam","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcomputational-cell-analytics%2Fmedico-sam","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcomputational-cell-analytics%2Fmedico-sam/lists"}