{"id":15987218,"url":"https://github.com/sbesson/embrc0001","last_synced_at":"2026-01-04T00:09:47.323Z","repository":{"id":145306860,"uuid":"146443139","full_name":"sbesson/embrc0001","owner":"sbesson","description":"Template repository for annotating EMBRC images","archived":false,"fork":false,"pushed_at":"2018-10-05T20:38:51.000Z","size":11,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-23T20:22:58.925Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sbesson.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-08-28T12:19:37.000Z","updated_at":"2018-10-05T20:38:53.000Z","dependencies_parsed_at":"2023-04-07T09:00:15.061Z","dependency_job_id":null,"html_url":"https://github.com/sbesson/embrc0001","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/sbesson%2Fembrc0001","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbesson%2Fembrc0001/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbesson%2Fembrc0001/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbesson%2Fembrc0001/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sbesson","download_url":"https://codeload.github.com/sbesson/embrc0001/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244020895,"owners_count":20385035,"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":"2024-10-08T03:21:57.863Z","updated_at":"2026-01-04T00:09:47.283Z","avatar_url":"https://github.com/sbesson.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"## Prerequisites\n\nCreate a Python virtual environment and install the prerequisites from the\n[requirements](requirements.txt) file:\n\n    virtualenv /tmp/venv\n    /tmp/venv/bin/pip install -r requirements.txt\n\n\nDownload OMERO.py from the [OMERO downloads](https://www.openmicroscopy.org/omero/downloads/) and extract it.\n\nActivate the virtual environment, and check the `metadata` command is\nregistered by the command-line interface shipped with OMERO.py:\n\n    /tmp/venv/bin/activate\n    cd /path/to/OMERO.py\n    bin/omero metadata -h\n\n## Annotating images\n\nThe image annotation is done in three steps:\n\n-   first an CSV file needs to be created containing the annotations.\n-   then the CSV file is converted into an OMERO.table attached to the\n    top-level Project. \n-   finally the OMERO.table can be converted into a series of map annotations\n    for each image.\n\n### Annotation file\n\nThis file can have as many columns as desired. For images in a Project/Dataset/Hierarchy, each row correspond to an image and two columns `Dataset Name` and `Image Name` are required to find the image.\n\n### Bulk annotations\n\nFirst create an OMERO.table (`bulk_annotations`) attached the top-level project from the [annotation.csv](annotation.csv) file:\n\n    bin/omero metadata populate --file annotation.csv Project:\u003cid\u003e\n\nWith OMERO 5.4.8, each row of this table should be viewable in the Web client\nby expanding the Tables tab on the right-hand panel of each image.\n\n### Map annotations\n\nThis conversion is done by a [configuration file](bulkmap.yml) which describes which columns should be turned into key/value pairs and whether some columns should be grouped together using a namespace e.g. Organism.\n\nRun the `metadata populate` command with the `bulkmap` context:\n\n    bin/omero metadata populate --context bulkmap --cfg bulkmap.yml Project:\u003cid\u003e\n\nThis should create map annotations for each image that can be viewed in the\nright-hand panel of the web client. Some of these annotations will have\nnamespaces allowing them to be searchable using the\n[OMERO.mapr](https://github.com/ome/omero-mapr) web app.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsbesson%2Fembrc0001","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsbesson%2Fembrc0001","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsbesson%2Fembrc0001/lists"}