{"id":29227323,"url":"https://github.com/royerlab/ultrack-i2k2023","last_synced_at":"2025-07-03T09:10:26.269Z","repository":{"id":200837940,"uuid":"706133482","full_name":"royerlab/ultrack-i2k2023","owner":"royerlab","description":"Ultrack https://github.com/royerlab/ultrack from Images to Knowledge - 2023 workshop","archived":false,"fork":false,"pushed_at":"2024-06-08T00:25:32.000Z","size":2388,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-06-08T01:34:35.708Z","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":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/royerlab.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":"2023-10-17T11:17:11.000Z","updated_at":"2024-06-08T00:25:17.000Z","dependencies_parsed_at":null,"dependency_job_id":"bb0f3d10-7668-4c5d-a5ce-73f135c66b12","html_url":"https://github.com/royerlab/ultrack-i2k2023","commit_stats":null,"previous_names":["royerlab/ultrack-i2k2023"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/royerlab/ultrack-i2k2023","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/royerlab%2Fultrack-i2k2023","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/royerlab%2Fultrack-i2k2023/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/royerlab%2Fultrack-i2k2023/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/royerlab%2Fultrack-i2k2023/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/royerlab","download_url":"https://codeload.github.com/royerlab/ultrack-i2k2023/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/royerlab%2Fultrack-i2k2023/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263296638,"owners_count":23444499,"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":"2025-07-03T09:10:25.576Z","updated_at":"2025-07-03T09:10:26.252Z","avatar_url":"https://github.com/royerlab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Ultrack Workshop I2K 2023\n\n[Ultrack](https://github.com/royerlab/ultrack) from Images to Knowledge - 2023 workshop\n\nThere are two options to follow this tutorial, locally or with Google Colab.\n\n## Local setup\n\nYou must have conda or mamba installed. If you don't have it, you can follow [their instructions](https://mamba.readthedocs.io/en/latest/mamba-installation.html#mamba-install).\n\nFirst, clone this repository:\n\n```bash\ngit clone https://github.com/royerlab/ultrack-i2k2023\n```\n\nGo to the repository folder:\n\n```bash\ncd ultrack-i2k2023\n```\n\nThen, you can create a new environment with the following command:\n\n```bash\nconda env create --file environment.yml\n```\n\nNOTE: If you're using apple silicon, you must use the `environment-apple.yml` file instead.\n\nThis will create a new environment called `ultrack-i2k2023`. You can activate it with:\n\n```bash\nconda activate ultrack-i2k2023\n```\n\nThen, you can browse the notebooks with:\n\n```bash\njupyter lab\n```\n\n## Google Colab\n\nFor Google Colab, you can follow the links below. You will need a Google account.\n\nTo access GPUs on Google Colab, you can go to `Runtime \u003e Change runtime type` and select `GPU` as the hardware accelerator.\n\n- Introduction:\n\n    https://colab.research.google.com/github/royerlab/ultrack-i2k2023/blob/main/intro.ipynb\n\n- Multiple hypotheses tracking:\n\n    https://colab.research.google.com/github/royerlab/ultrack-i2k2023/blob/main/multiple-labels.ipynb\n\n\n## Additional Resources\n\nFor best performance we recommend using `gurobi`. It's a commercial software, but it's free for academic use. You can get a license [here](https://www.gurobi.com/academia/academic-program-and-licenses/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Froyerlab%2Fultrack-i2k2023","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Froyerlab%2Fultrack-i2k2023","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Froyerlab%2Fultrack-i2k2023/lists"}