{"id":19721983,"url":"https://github.com/datajoint/workflow-miniscope","last_synced_at":"2026-03-12T23:32:16.739Z","repository":{"id":40500751,"uuid":"350499051","full_name":"datajoint/workflow-miniscope","owner":"datajoint","description":"Example DataJoint workflow for miniscope calcium imaging analysis with CaImAn","archived":false,"fork":false,"pushed_at":"2023-05-18T16:14:54.000Z","size":1153,"stargazers_count":2,"open_issues_count":1,"forks_count":9,"subscribers_count":10,"default_branch":"main","last_synced_at":"2025-04-29T22:36:23.382Z","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,"zenodo":null}},"created_at":"2021-03-22T21:48:13.000Z","updated_at":"2023-01-11T14:24:13.000Z","dependencies_parsed_at":"2025-04-29T22:41:27.618Z","dependency_job_id":null,"html_url":"https://github.com/datajoint/workflow-miniscope","commit_stats":null,"previous_names":[],"tags_count":3,"template":true,"template_full_name":null,"purl":"pkg:github/datajoint/workflow-miniscope","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datajoint%2Fworkflow-miniscope","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datajoint%2Fworkflow-miniscope/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datajoint%2Fworkflow-miniscope/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datajoint%2Fworkflow-miniscope/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/datajoint","download_url":"https://codeload.github.com/datajoint/workflow-miniscope/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datajoint%2Fworkflow-miniscope/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30449074,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-12T21:31:01.033Z","status":"ssl_error","status_checked_at":"2026-03-12T21:30:43.161Z","response_time":114,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":[],"created_at":"2024-11-11T23:16:08.275Z","updated_at":"2026-03-12T23:32:16.716Z","avatar_url":"https://github.com/datajoint.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DataJoint Workflow for Miniscope Calcium Imaging\n\nThe DataJoint Workflow for miniscope calcium imaging data acquired with miniature\nmicroscopes (e.g. [UCLA Miniscope](https://github.com/Aharoni-Lab/Miniscope-v4)) using\nthe [Miniscope-DAQ](https://github.com/Aharoni-Lab/Miniscope-DAQ-QT-Software)\nacquisition software and processed with\n[CaImAn](https://github.com/flatironinstitute/CaImAn). DataJoint Elements collectively\nstandardize and automate data collection and analysis for neuroscience experiments. Each\nElement is a modular pipeline for data storage and processing with corresponding\ndatabase tables that can be combined with other Elements to assemble a fully functional\npipeline.  This repository also provides a tutorial notebook to learn the pipeline.\n\n## Experiment Flowchart\n\n![flowchart](https://raw.githubusercontent.com/datajoint/element-miniscope/main/images/flowchart.svg)\n\n## Data Pipeline Diagram\n\n![pipeline](https://raw.githubusercontent.com/datajoint/element-miniscope/main/images/pipeline_imaging.svg)\n\n## Getting Started\n\n+ [Interactive tutorial](#interactive-tutorial)\n\n+ Install Element Miniscope from PyPI\n\n     ```bash\n     pip install element-miniscope\n     ```\n\n+ [Documentation](https://datajoint.com/docs/elements/element-miniscope)\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  + Install [Mamba](https://mamba.readthedocs.io/en/latest/installation.html)\n  + Install [CaImAn](https://caiman.readthedocs.io/en/master/Installation.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 `miniscope_root_data_dir`. See [User Guide](https://datajoint.com/docs/elements/user-guide/) for details.\n  + Add your example data to the `miniscope_root_data_dir`.\n\n### Instructions\n\n1. We recommend you start by navigating to the `notebooks` directory. Execute the cells in the notebooks to begin your walk through of the tutorial.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatajoint%2Fworkflow-miniscope","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatajoint%2Fworkflow-miniscope","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatajoint%2Fworkflow-miniscope/lists"}