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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":"2024-11-11T23:16:01.820Z","updated_at":"2026-03-10T21:32:49.138Z","avatar_url":"https://github.com/datajoint.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DataJoint Element for Functional Calcium Imaging\n\nDataJoint Element for functional calcium imaging with support for\n[ScanImage](https://docs.scanimage.org/), [Scanbox](https://scanbox.org/), [Nikon\nNIS-Elements](https://www.microscope.healthcare.nikon.com/products/software/nis-elements),\nand `Bruker Prairie View` acquisition software; and\n[Suite2p](https://github.com/MouseLand/suite2p),\n[CaImAn](https://github.com/flatironinstitute/CaImAn), and\n[EXTRACT](https://github.com/schnitzer-lab/EXTRACT-public) analysis software. DataJoint\nElements collectively standardize and automate data collection and analysis for\nneuroscience experiments. Each Element is a modular pipeline for data storage and\nprocessing with corresponding database tables that can be combined with other Elements\nto assemble a fully functional pipeline. This repository also provides a tutorial\nenvironment and notebooks to learn the pipeline.\n\n## Experiment Flowchart\n\n![flowchart](https://raw.githubusercontent.com/datajoint/element-calcium-imaging/main/images/flowchart.svg)\n\n## Data Pipeline Diagram\n\n![pipeline](https://raw.githubusercontent.com/datajoint/element-calcium-imaging/main/images/pipeline_imaging_no_curation.svg)\n\n### Legacy Support\n\n+ Three variations of the pipeline were designed and supported through December 2024 to\n  handle different use cases. However, based on community feedback and use cases, only\n  one pipeline will be supported after December 2024. However, all three pipeline\n  versions will remain available in their own branches for reference and use.\n+ Displayed above is the default `imaging` schema. Please see other branches for the\n  `imaging` module with `Curation` table and the `imaging_preprocess` module.\n\n## Getting Started\n\n+ Please fork this repository\n\n+ Clone the repository to your computer\n\n  ```bash\n  git clone https://github.com/\u003center_github_username\u003e/element-calcium-imaging.git\n  ```\n\n+ Install with `pip`\n\n  ```bash\n  pip install -e .\n  ```\n\n+ [Interactive tutorial on GitHub Codespaces](#interactive-tutorial)\n\n+ [Documentation](https://datajoint.com/docs/elements/element-calcium-imaging)\n\n## Support\n\n+ If you need help getting started or run into any errors, please open a GitHub Issue \nor contact our team by email at support@datajoint.com.\n\n## Interactive Tutorial\n\n+ The easiest way to learn about DataJoint Elements is to use the tutorial notebooks\n  within the included interactive environment configured using [Dev\n  Container](https://containers.dev/).\n\n### Launch Environment\n\nHere are some options that provide a great experience:\n\n+ (*recommended*) Cloud-based Environment\n  + Launch using [GitHub Codespaces](https://github.com/features/codespaces) using the\n    `+` option which will `Create codespace on main` in the codebase repository on your\n    fork with default options. For more control, see the `...` where you may create `New\n    with options...`.\n  + Build time for a codespace is a few minutes. This is done infrequently and cached\n    for convenience.\n  + Start time for a codespace is less than 1 minute. This will pull the built codespace\n    from cache when you need it.\n  + *Tip*: Each month, GitHub renews a\n    [free-tier](https://docs.github.com/en/billing/managing-billing-for-github-codespaces/about-billing-for-github-codespaces#monthly-included-storage-and-core-hours-for-personal-accounts)\n    quota of compute and storage. Typically we run into the storage limits before\n    anything else since Codespaces consume storage while stopped. It is best to delete\n    Codespaces when not actively in use and recreate when needed. We'll soon be creating\n    prebuilds to avoid larger build times. Once any portion of your quota is reached,\n    you will need to wait for it to be reset at the end of your cycle or add billing\n    info to your GitHub account to handle overages.\n  + *Tip*: GitHub auto names the codespace but you can rename the codespace so that it\n    is easier to identify later.\n\n+ Local Environment\n  \u003e *Note: Access to example data is currently limited to MacOS and Linux due to the\n  \u003e s3fs utility. Windows users are recommended to use the above environment.*\n  + Install [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)\n  + Install [Docker](https://docs.docker.com/get-docker/)\n  + Install [VSCode](https://code.visualstudio.com/)\n  + Install the VSCode [Dev Containers\n    extension](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers)\n  + `git clone` the codebase repository and open it in VSCode\n  + Use the `Dev Containers extension` to `Reopen in Container` (More info is in the\n    `Getting started` included with the extension.)\n\nYou will know your environment has finished loading once you either see a terminal open\nrelated to `Running postStartCommand` with a final message of `Done` or the `README.md`\nis opened in `Preview`.\n\nOnce the environment has launched, please run the following command in the terminal:\n```sh\nMYSQL_VER=8.0 docker compose -f docker-compose-db.yaml up --build -d\n```\n\n### Instructions\n\n1. We recommend you start by navigating to the `notebooks` directory on the left panel\n   and go through the `tutorial.ipynb` Jupyter notebook. Execute the cells in the\n   notebook to begin your walk through of the tutorial.\n\n2. Once you are done, see the options available to you in the menu in the bottom-left\n   corner. For example, in Codespace you will have an option to `Stop Current Codespace`\n   but when running Dev Container on your own machine the equivalent option is `Reopen\n   folder locally`. By default, GitHub will also automatically stop the Codespace after\n   30 minutes of inactivity.  Once the Codespace is no longer being used, we recommend\n   deleting the Codespace.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatajoint%2Felement-calcium-imaging","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatajoint%2Felement-calcium-imaging","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatajoint%2Felement-calcium-imaging/lists"}