{"id":19721977,"url":"https://github.com/datajoint/workflow-zstack","last_synced_at":"2025-02-27T18:28:15.780Z","repository":{"id":148763293,"uuid":"605153941","full_name":"datajoint/workflow-zstack","owner":"datajoint","description":"Example DataJoint workflow for volumetric data analysis using BossDB","archived":false,"fork":false,"pushed_at":"2023-10-03T14:03:12.000Z","size":124,"stargazers_count":0,"open_issues_count":0,"forks_count":3,"subscribers_count":8,"default_branch":"main","last_synced_at":"2025-01-10T16:23:07.131Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://datajoint.com/docs","language":"Jupyter Notebook","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/datajoint.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","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":"2023-02-22T15:03:01.000Z","updated_at":"2023-05-19T20:58:51.000Z","dependencies_parsed_at":"2025-01-16T03:13:29.040Z","dependency_job_id":null,"html_url":"https://github.com/datajoint/workflow-zstack","commit_stats":null,"previous_names":[],"tags_count":0,"template":true,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datajoint%2Fworkflow-zstack","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datajoint%2Fworkflow-zstack/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datajoint%2Fworkflow-zstack/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datajoint%2Fworkflow-zstack/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/datajoint","download_url":"https://codeload.github.com/datajoint/workflow-zstack/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241044199,"owners_count":19899478,"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":"2024-11-11T23:16:08.189Z","updated_at":"2025-02-27T18:28:15.755Z","avatar_url":"https://github.com/datajoint.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DataJoint Workflow for ZStack Imaging\n\nThe DataJoint Workflow for ZStack Imaging combines five DataJoint Elements for\nvolume cell segmentation - Elements Lab, Animal, Session, Calcium Imaging, and\nZStack. DataJoint Elements collectively standardize and automate data collection\nand analysis for neuroscience experiments. Each Element is a modular pipeline for data \nstorage and processing with corresponding database tables that can be combined with\nother Elements to assemble a fully functional pipeline. This repository also provides \na tutorial environment and notebook to learn the pipeline.\n\n## Experiment Flowchart\n\n![flowchart](https://raw.githubusercontent.com/datajoint/element-zstack/main/images/flowchart.svg)\n\n## Data Pipeline Diagram\n\n![pipeline](https://raw.githubusercontent.com/datajoint/element-zstack/main/images/pipeline.svg)\n\n## Getting Started\n\n+ [Interactive tutorial](#interactive-tutorial)\n\n+ Install Element ZStack from PyPI\n\n     ```bash\n     pip install element-zstack\n     ```\n\n+ [Documentation](https://datajoint.com/docs/elements/element-zstack)\n\n## Support\n\n+ If you need help getting started or run into any errors, please contact our team by email at support@datajoint.com.\n\n## Interactive Tutorial\n\n### Launch Environment\n\n+ Local Environment\n  + Install [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)\n  + Install [VSCode](https://code.visualstudio.com/)\n  + Install [Conda](https://docs.conda.io/en/latest/miniconda.html)\n  + Configure a database.  See [here](https://tutorials.datajoint.org/setting-up/local-database.html) for details.\n  + `git clone` the code repository and open it in VSCode\n  + Install the repository with `pip install -e .`\n  + Setup a `dj_local_conf.json` with the `database.prefix` and `volume_root_data_dir`. See [User Guide](https://datajoint.com/docs/elements/user-guide/) for details.\n  + Add your example data to the `volume_root_data_dir`.\n\n### Instructions\n\n1. To upload data to BossDB, [create an account](https://api.bossdb.io) to\n   access the BossDB API and generate an API token. Please contact the team at [BossDB](https://bossdb.org)\n   to ensure you have `resource-manager` permissions for your account. \n2. Follow the instructions below to set up the\n   [intern](https://github.com/jhuapl-boss/intern) REST API locally. \n   + Create a new folder `.intern` in your user directory.\n   + Create a configuration file `intern.cfg` within the `.intern` folder. The\n     path to this file should be `~/.intern/intern.cfg`. \n   + The `intern.cfg` file should contain the following exactly as shown below:\n   ```bash\n    # ~/.intern/intern.cfg\n    [Default]\n    protocol = https\n    host = api.bossdb.io\n    token = \u003cyour-api-key\u003e\n   ```\n3. Use the instructions above to set up a local environment.\n4. Navigate to the `notebooks` directory. Execute the cells in the notebooks to begin your walk through of the tutorial.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatajoint%2Fworkflow-zstack","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatajoint%2Fworkflow-zstack","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatajoint%2Fworkflow-zstack/lists"}