{"id":22631915,"url":"https://github.com/alleninstitute/ophys_nway_matching","last_synced_at":"2025-06-19T06:33:47.255Z","repository":{"id":45742305,"uuid":"200717177","full_name":"AllenInstitute/ophys_nway_matching","owner":"AllenInstitute","description":null,"archived":false,"fork":false,"pushed_at":"2023-11-03T00:45:22.000Z","size":1598,"stargazers_count":4,"open_issues_count":8,"forks_count":0,"subscribers_count":8,"default_branch":"main","last_synced_at":"2025-06-15T07:49:08.768Z","etag":null,"topics":[],"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/AllenInstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-08-05T19:34:23.000Z","updated_at":"2023-07-20T13:38:19.000Z","dependencies_parsed_at":"2023-10-20T16:43:28.453Z","dependency_job_id":"a6583ab6-4552-4b69-9167-8d561ad00679","html_url":"https://github.com/AllenInstitute/ophys_nway_matching","commit_stats":{"total_commits":155,"total_committers":3,"mean_commits":"51.666666666666664","dds":0.05161290322580647,"last_synced_commit":"545504ab55922717ab623f8ede2c521a60aa1458"},"previous_names":[],"tags_count":10,"template":false,"template_full_name":null,"purl":"pkg:github/AllenInstitute/ophys_nway_matching","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fophys_nway_matching","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fophys_nway_matching/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fophys_nway_matching/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fophys_nway_matching/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AllenInstitute","download_url":"https://codeload.github.com/AllenInstitute/ophys_nway_matching/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fophys_nway_matching/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260702247,"owners_count":23049204,"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":"2024-12-09T02:14:11.676Z","updated_at":"2025-06-19T06:33:42.233Z","avatar_url":"https://github.com/AllenInstitute.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![CircleCI](https://circleci.com/gh/AllenInstitute/ophys_nway_matching.svg?style=svg)](https://circleci.com/gh/AllenInstitute/ophys_nway_matching)\n[![codecov](https://codecov.io/gh/AllenInstitute/ophys_nway_matching/branch/master/graph/badge.svg?token=y5Nt5RnMwB)](https://codecov.io/gh/AllenInstitute/ophys_nway_matching)\n\n# ophys_nway_matching\nN-way matching of segmented cell ROIs\n\n# Docker and Singularity\nA docker image is built in CircleCI and pushed to [dockerhub](https://hub.docker.com/repository/docker/alleninstitutepika/ophys_nway_matching) tagged as either `master` or `develop`.\n\nSingularity should be able to run this docker image directly:\n```\nsingularity run docker://alleninstitutepika/ophys_nway_matching:develop python -m pytest /ophys_nway_matching\n```\nor\n```\nsingularity run docker://alleninstitutepika/ophys_nway_matching:develop python -m nway.nway_matching --help\n```\n\nIt appears the calling singularity in this way intelligently uses the local caches for both docker and singularity. There is an overhead for downloading an updated docker image and translating it to a singularity image. That cost is incurred only when the docker image has changed.\n\n# quick start\n\n```\nconda create -n nwaytest python=3.6.4\nconda activate nwaytest\npip install git+https://github.com/AllenInstitute/ophys_nway_matching\npython -m nway.nway_matching --input_json tmp_example/input.json --output_json tmp_example/output.json\n```\n\nThis creates `tmp_example/output.json`. The intent is that this file contains everything you need to know, both results and diagnostic metrics.\n\nSome basic visualizations of the results are in `nway.diagnostics`\n```\npython -m nway.diagnostics --input_json tmp_example/output.json --output_pdf tmp_example/output.pdf\n\n```\n\nThis should create `tmp_example/output.pdf`.\n\n# Level of support\nWe are not currently supporting this code, but simply releasing it to the community AS IS but are not able to provide any guarantees of support, as it is under active development. The community is welcome to submit issues, but you should not expect an active response.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falleninstitute%2Fophys_nway_matching","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falleninstitute%2Fophys_nway_matching","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falleninstitute%2Fophys_nway_matching/lists"}