{"id":23951324,"url":"https://github.com/psteinb/b3get","last_synced_at":"2025-04-12T23:42:05.504Z","repository":{"id":57413586,"uuid":"170895677","full_name":"psteinb/b3get","owner":"psteinb","description":"a python module to download Broad Bioimage Benchmark Collection images","archived":false,"fork":false,"pushed_at":"2019-03-15T14:44:49.000Z","size":166,"stargazers_count":24,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-12T23:42:01.647Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/psteinb.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.rst","contributing":"CONTRIBUTING.rst","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-02-15T16:33:10.000Z","updated_at":"2023-05-18T22:38:10.000Z","dependencies_parsed_at":"2022-09-15T03:26:04.208Z","dependency_job_id":null,"html_url":"https://github.com/psteinb/b3get","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/psteinb%2Fb3get","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/psteinb%2Fb3get/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/psteinb%2Fb3get/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/psteinb%2Fb3get/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/psteinb","download_url":"https://codeload.github.com/psteinb/b3get/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248647257,"owners_count":21139081,"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":"2025-01-06T12:59:30.499Z","updated_at":"2025-04-12T23:42:05.481Z","avatar_url":"https://github.com/psteinb.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# b3get [![Build Status](https://travis-ci.com/psteinb/b3get.svg?branch=master)](https://travis-ci.com/psteinb/b3get) [![codecov](https://codecov.io/gh/psteinb/b3get/branch/master/graph/badge.svg)](https://codecov.io/gh/psteinb/b3get)\n\nA python module to download [Broad Bioimage Benchmark Collection](https://data.broadinstitute.org/bbbc/image_sets.html) images.\n\n## Usage\n\n### As a python module\n\n``` python\nimport b3get\n\nimages, labels = b3get.to_numpy(6)\n```\nThe call illustrated above creates 2 python lists. Each list contains a set of `numpy.ndarray` objects which yield the images of the dataset (`images`) or the labels (`labels`). \n\nIf you like the idea for this repo, please drop me a star. Due to time constraints, I will concentrate on dataset [06](https://data.broadinstitute.org/bbbc/BBBC006/), [24](https://data.broadinstitute.org/bbbc/BBBC024/) and [27](https://data.broadinstitute.org/bbbc/BBBC027/). If your dataset is not among those, please consider contributing.\n\n### From the Command-line\n\n- to list available datasets\n\n``` shell\n$ b3get list\nBBBC006 Human U2OS cells (out of focus) \nBBBC008 Human HT29 colon-cancer cells   \nBBBC024 3D HL60 Cell Line (synthetic data)\nBBBC027 3D Colon Tissue (synthetic data)\n```\n\n- to show the URLS for a given dataset\n\n``` shell\n$ b3get show 08\nhttps://data.broadinstitute.org/bbbc/BBBC008/BBBC008_v1_images.zip\nhttps://data.broadinstitute.org/bbbc/BBBC008/BBBC008_v1_foreground.zip\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpsteinb%2Fb3get","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpsteinb%2Fb3get","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpsteinb%2Fb3get/lists"}