{"id":19129921,"url":"https://github.com/mathworks/open-microscopy-data-matlab","last_synced_at":"2025-11-13T05:02:32.341Z","repository":{"id":210890150,"uuid":"727687946","full_name":"mathworks/Open-Microscopy-Data-MATLAB","owner":"mathworks","description":"Access open microscopy data in MATLAB and create reproducible code","archived":false,"fork":false,"pushed_at":"2024-04-25T09:30:59.000Z","size":39564,"stargazers_count":2,"open_issues_count":0,"forks_count":2,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-02-22T16:56:49.649Z","etag":null,"topics":["open-data","open-science"],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mathworks.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":"SECURITY.md","support":null,"governance":null,"roadmap":null,"authors":null}},"created_at":"2023-12-05T11:22:34.000Z","updated_at":"2024-07-10T16:16:04.000Z","dependencies_parsed_at":"2023-12-15T08:37:28.544Z","dependency_job_id":null,"html_url":"https://github.com/mathworks/Open-Microscopy-Data-MATLAB","commit_stats":null,"previous_names":["mathworks/open-microscopy-data-matlab"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/mathworks/Open-Microscopy-Data-MATLAB","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mathworks%2FOpen-Microscopy-Data-MATLAB","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mathworks%2FOpen-Microscopy-Data-MATLAB/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mathworks%2FOpen-Microscopy-Data-MATLAB/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mathworks%2FOpen-Microscopy-Data-MATLAB/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mathworks","download_url":"https://codeload.github.com/mathworks/Open-Microscopy-Data-MATLAB/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mathworks%2FOpen-Microscopy-Data-MATLAB/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":284156474,"owners_count":26956828,"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","status":"online","status_checked_at":"2025-11-13T02:00:06.582Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["open-data","open-science"],"created_at":"2024-11-09T06:09:00.959Z","updated_at":"2025-11-13T05:02:32.324Z","avatar_url":"https://github.com/mathworks.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![View Open-Microscopy-Data-MATLAB on File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://www.mathworks.com/matlabcentral/fileexchange/156034-open-microscopy-data-matlab)\n[![Open in MATLAB Online](https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg)](https://matlab.mathworks.com/open/github/v1?repo=mathworks/Open-Microscopy-Data-MATLAB\u0026file=OpenBiologyTutorial.mlx)\n# Analyse Open Microscopy Data in MATLAB®\n\nA MATLAB Live Script with accompanying \n- [Jupyter® Notebook](https://github.com/mathworks/Open-Microscopy-Data-MATLAB/blob/main/OpenBiologyTutorial.ipynb), \n- [m file](https://github.com/mathworks/Open-Microscopy-Data-MATLAB/blob/9d6ed32395816ae334ac5e917b5d4a0e68ed292d/OpenBiologyTutorialScript.m)and \n- [reproducible code capsule on Code Ocean®](https://doi.org/10.24433/CO.8820386.v1)\n\nto access and analyze Microscopy image data sets from the Image Data Resource database\n\n## Get started\n\nUse this tutorial to get started with freely available microscopy data at [Image Data Resource](https://idr.openmicroscopy.org/) directly from MATLAB.\n- No downloads, no installations\n- **Open directly in MATLAB Online™** by clicking this [![Open in MATLAB Online](https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg)](https://matlab.mathworks.com/open/github/v1?repo=mathworks/Open-Microscopy-Data-MATLAB\u0026file=OpenBiologyTutorial.mlx)\n- Step-by-step tutorial shows how to\n    - Re-use available data. **Access a list of openly available projects** on Open Microscopy\n    - **Query and inspect the metadata** associated with these projects using commands directly from MATLAB (RESTful API)\n    - Avoid downloads. **Access specific data** from within the database directly and **avoid time-consuming downloads** of large data\n    - **Analyze image data** to identify cells\n    - Let others run your code and reproduce your results quickly. **Pubish the results on GitHub** and **make them accessible** using Open With MATLAB Online\n    - Allow people to cite you! **Generate a DOI®** for your code by linking your GitHub repository to one of several DOI-generating sites.\n- **Live Script** contains **easy-to-use menus** for user to click and select different datasets\n- Available on [File Exchange](https://www.mathworks.com/matlabcentral/fileexchange/) for directly installing onto your MATLAB path with one click using the [Add-Ons button](https://www.mathworks.com/help/matlab/matlab_env/get-add-ons.html)\n- Accompanying **Jupyter notebook** (.ipynb) for use in a Jupyter environment. More information on MATLAB kernel [here](https://www.mathworks.com/products/reference-architectures/jupyter.html)\n- Accompanying [**Code Ocean® reproducible capsule** (.m)](https://doi.org/10.24433/CO.8820386.v1) for one-click reproducibility of the code by anyone, including reviewers.\n\n## About the Image Data Resource\nThe Image Data Resource (IDR) is a public repository of image datasets from published scientific studies, where the community can submit, search and access high-quality bio-image data.\nIt can be accessed at [https://idr.openmicroscopy.org/](https://idr.openmicroscopy.org/)\n\n**For advanced users** A detailed guide to the Image Data Resource API can be found [here](https://idr.openmicroscopy.org/about/api.html). To access the REST API use the MATLAB [webread](https://www.mathworks.com/help/matlab/ref/webread.html) function\n\n### Required Products\nThis tutorial uses the following products\n- MATLAB\n- Image Processing Toolbox \u0026trade;\n\nThis code has been developed and tested using MATLAB 2023b\n\n**Note**\nThis tutorial works best when delivered by a tutor. It is important to highlight best practices when working with Open Data, publishing Open Code or making research output reproducible\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmathworks%2Fopen-microscopy-data-matlab","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmathworks%2Fopen-microscopy-data-matlab","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmathworks%2Fopen-microscopy-data-matlab/lists"}