{"id":18454735,"url":"https://github.com/vitessce/vitessce-python-tutorial","last_synced_at":"2025-04-08T04:33:51.213Z","repository":{"id":65325922,"uuid":"587768175","full_name":"vitessce/vitessce-python-tutorial","owner":"vitessce","description":"Notebooks for HuBMAP tutorial session (January 2023)","archived":false,"fork":false,"pushed_at":"2023-06-29T18:59:24.000Z","size":58785,"stargazers_count":7,"open_issues_count":4,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-23T06:11:20.408Z","etag":null,"topics":["gehlenborglab","hidivelab","single-cell","vitessce"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vitessce.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2023-01-11T14:42:26.000Z","updated_at":"2025-03-09T20:36:57.000Z","dependencies_parsed_at":"2023-02-16T23:15:21.003Z","dependency_job_id":null,"html_url":"https://github.com/vitessce/vitessce-python-tutorial","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vitessce%2Fvitessce-python-tutorial","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vitessce%2Fvitessce-python-tutorial/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vitessce%2Fvitessce-python-tutorial/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vitessce%2Fvitessce-python-tutorial/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vitessce","download_url":"https://codeload.github.com/vitessce/vitessce-python-tutorial/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247779796,"owners_count":20994569,"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":["gehlenborglab","hidivelab","single-cell","vitessce"],"created_at":"2024-11-06T08:05:56.568Z","updated_at":"2025-04-08T04:33:48.443Z","avatar_url":"https://github.com/vitessce.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# vitessce-python-tutorial\n\nThis tutorial will teach you how to use the `vitessce` python package to construct Vitessce configurations for local datasets.\n\n\u003cdiv style=\"display: flex; flex-direction: column;\"\u003e\n\u003cimg src=\"./.github/img/screenshot02.png\" width=\"400\" /\u003e\n\u003cimg src=\"./.github/img/screenshot04.png\" width=\"400\" /\u003e\n\u003cimg src=\"./.github/img/screenshot05.png\" width=\"400\"/\u003e\n\u003cimg src=\"./.github/img/screenshot06.png\" width=\"400\"/\u003e\n\u003c/div\u003e\n\n### Examples\n\nThe example notebooks in `examples/` demonstrate the types of visualizations that are possible to create with Vitessce. These contain minimal examples of each data type, and they point to remote data so that they can be executed in cloud notebook environments such as Google Colab.\n\n### Tutorials\n\nThe tutorial notebooks in `tutorials/` demonstrate required data processing and conversion steps, visualization configuration, and data/configuration exporting.\n\n### Templates\n\nThe template notebooks in `templates/` contain fill-in-the-blank comments for adapting them to your own data. They contain fewer explanations and descriptions than the tutorial notebooks, and the three steps of data processing, visualization configuration, and exporting are merged rather than split across different notebooks.\n\n## Setup\n\nPrerequisites:\n- [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) installation\n- familiarity with Python code and Jupyter notebooks\n- familiarity with using the command line (e.g., installing command line tools, downloading files)\n\nSet up the Python environment using conda:\n\n```sh\nconda env create -f environment.yml\n```\n\n### Image data processing (optional)\n\nTo convert image data into OME-TIFF format, you will want to install [`bftools`](https://docs.openmicroscopy.org/bio-formats/latest/users/comlinetools/index.html) by unzipping it. My installation is located at `~/software/bftools`.\n\n\n## Run notebooks\n\nActivate the environment:\n\n```sh\nconda activate vitessce-tutorial-env\n```\n\nLaunch JupyterLab in the sub-directory of interest:\n\n```sh\njupyter lab --notebook-dir=./tutorials/transcriptomics\n# or\njupyter lab --notebook-dir=./tutorials/imaging\n# or\njupyter lab --notebook-dir=./tutorials/spatial_single_cell\n# or\njupyter lab --notebook-dir=./templates\n```\n\nTo download the raw data for the tutorials, run the following notebooks:\n\n- `./tutorials/transcriptomics/raw_data/download.ipynb`\n- `./tutorials/spatial_single_cell/raw_data/download.ipynb`\n\n## Additional resources\n\n- [Vitessce demo data processing scripts](https://github.com/vitessce/vitessce-python/tree/main/demos)\n\n## References\n\nRaw data:\n- Transcriptomics data from https://www.covid19cellatlas.org/index.healthy.html#habib17\n- Visium data from https://scanpy.readthedocs.io/en/stable/generated/scanpy.datasets.visium_sge.html#scanpy.datasets.visium_sge\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvitessce%2Fvitessce-python-tutorial","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvitessce%2Fvitessce-python-tutorial","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvitessce%2Fvitessce-python-tutorial/lists"}