{"id":19215889,"url":"https://github.com/vanvalenlab/deepcell-datasets","last_synced_at":"2025-08-17T10:05:26.212Z","repository":{"id":39004426,"uuid":"263134532","full_name":"vanvalenlab/deepcell-datasets","owner":"vanvalenlab","description":"React App for hosting curated datasets.","archived":false,"fork":false,"pushed_at":"2023-06-26T23:03:03.000Z","size":16856,"stargazers_count":0,"open_issues_count":18,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-01-04T18:31:50.561Z","etag":null,"topics":["react","serverless"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vanvalenlab.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":"2020-05-11T19:13:27.000Z","updated_at":"2021-12-20T22:50:26.000Z","dependencies_parsed_at":"2025-01-04T18:38:54.058Z","dependency_job_id":null,"html_url":"https://github.com/vanvalenlab/deepcell-datasets","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/vanvalenlab%2Fdeepcell-datasets","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vanvalenlab%2Fdeepcell-datasets/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vanvalenlab%2Fdeepcell-datasets/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vanvalenlab%2Fdeepcell-datasets/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vanvalenlab","download_url":"https://codeload.github.com/vanvalenlab/deepcell-datasets/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240292512,"owners_count":19778310,"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":["react","serverless"],"created_at":"2024-11-09T14:15:10.203Z","updated_at":"2025-02-23T08:40:28.040Z","avatar_url":"https://github.com/vanvalenlab.png","language":"Python","readme":"# DeepCell Datasets\n\n[![Actions Status](https://github.com/vanvalenlab/deepcell-datasets/workflows/Test%20API/badge.svg)](https://github.com/vanvalenlab/deepcell-datasets/actions)\n[![Coverage Status](https://coveralls.io/repos/github/vanvalenlab/deepcell-datasets/badge.svg)](https://coveralls.io/github/vanvalenlab/deepcell-datasets)\n\n## Getting Started\n\nDeepCell Datasets is a serverless applicatioin that allows authenticated users to access published datasets.\nThis is aided by using `lerna` as well as the `serverless` framework.\n`lerna` enables us to easily control all of the services from the root directory, while `serverless` allows us to deploy and manage AWS infrastructure through `.yml` configuration files.\n\nMake sure serverless is installed by running `npm install -g serverless@2`.\n\n### Deployment\n\n`lerna` is used to manage and deploy both the frontend and the application services with a simple `yarn` or `npm` command:\n\n```bash\nyarn deploy:dev\n# yarn deploy:prod\n```\n\n### Architecture\n\nThe application implements a microservice architecture made up of the following components:\n\n- [`frontend`](frontend/): a static webpage that is the primary interface of the application.\n- [AWS Congito](https://aws.amazon.com/cognito): An AWS service that handles all user authentication. Users that have confirmed their email address are authenticated to download data in a protected S3 bucket. The authentication React components have been overridden in `frontend/src/auth` to provide the application with a cohesive style.\n- [`send-email`](services/send-email): an AWS Lambda service that can send email to admins on behalf of new users.\n- [`validate-email-domain`](services/validate-email-domain): a deprecated service that whitelists certain domains for account creation. This is used as a pre-signup hook for AWS Cognito.\n\n### How to update with new data\n\nData is saved in a protected S3 bucket, but to enable users to view and download these datasets, the details must be saved in [`frontend/src/datasets/AllDatasets.tsx`](frontend/src/datasets/AllDatasets.tsx).\n\nThis is a simple JSON object that has the following fields:\n\n| Name              | Description                                                                         |\n| :---------------- | :---------------------------------------------------------------------------------- |\n| `title`           | The name of the dataset.                                                            |\n| `objectKey`       | The path to the dataset inside the S3 bucket.                                       |\n| `thumbnail`       | The path to the thumbnail example, which must be saved in `frontend/public/images`. |\n| `imagingPlatform` | The imaging platform that created the dataset.                                      |\n| `samples`         | The type of image data.                                                             |\n| `description`     | A brief description of the data.                                                    |\n\n## Copyright\n\nCopyright © 2016-2021 [The Van Valen Lab](http://www.vanvalen.caltech.edu/) at the California Institute of Technology (Caltech), with support from the Paul Allen Family Foundation, Google, \u0026 National Institutes of Health (NIH) under Grant U24CA224309-01.\nAll rights reserved.\n\n## License\n\nThis software is licensed under a modified [APACHE2](LICENSE).\n\n[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)\n\nSee [LICENSE](LICENSE) for full details.\n\n## Trademarks\n\nAll other trademarks referenced herein are the property of their respective owners.\n\n## Credits\n\n[![Van Valen Lab, Caltech](https://upload.wikimedia.org/wikipedia/commons/7/75/Caltech_Logo.svg)](http://www.vanvalen.caltech.edu/)\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvanvalenlab%2Fdeepcell-datasets","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvanvalenlab%2Fdeepcell-datasets","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvanvalenlab%2Fdeepcell-datasets/lists"}