{"id":28205202,"url":"https://github.com/ome/omero-iviewer","last_synced_at":"2025-06-14T12:30:57.520Z","repository":{"id":14016050,"uuid":"75535262","full_name":"ome/omero-iviewer","owner":"ome","description":"An OMERO.web app allowing to view images","archived":false,"fork":false,"pushed_at":"2025-05-23T12:21:46.000Z","size":11871,"stargazers_count":19,"open_issues_count":70,"forks_count":30,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-06-05T16:27:23.930Z","etag":null,"topics":["omero","webapp"],"latest_commit_sha":null,"homepage":"https://www.openmicroscopy.org/omero/iviewer/","language":"JavaScript","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/ome.png","metadata":{"files":{"readme":"README.rst","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":"SUPPORT.md","governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2016-12-04T12:13:15.000Z","updated_at":"2025-05-23T12:21:50.000Z","dependencies_parsed_at":"2024-04-16T04:41:04.442Z","dependency_job_id":"9df2ad9e-2ada-423a-b00d-2ec0487ce735","html_url":"https://github.com/ome/omero-iviewer","commit_stats":{"total_commits":1753,"total_committers":11,"mean_commits":"159.36363636363637","dds":0.5733029092983457,"last_synced_commit":"a8f380fabfd839b946e5a5f613f1fce07abb3815"},"previous_names":[],"tags_count":29,"template":false,"template_full_name":null,"purl":"pkg:github/ome/omero-iviewer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ome%2Fomero-iviewer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ome%2Fomero-iviewer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ome%2Fomero-iviewer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ome%2Fomero-iviewer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ome","download_url":"https://codeload.github.com/ome/omero-iviewer/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ome%2Fomero-iviewer/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259816180,"owners_count":22915827,"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":["omero","webapp"],"created_at":"2025-05-17T08:13:53.558Z","updated_at":"2025-06-14T12:30:57.512Z","avatar_url":"https://github.com/ome.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":".. image:: https://github.com/ome/omero-iviewer/workflows/OMERO/badge.svg\n    :target: https://github.com/ome/omero-iviewer/actions\n\n.. image:: https://badge.fury.io/py/omero-iviewer.svg\n    :target: https://badge.fury.io/py/omero-iviewer\n\nOMERO.iviewer\n=============\n\nAn OMERO.web app for visualizing images in OMERO.\n\nAlso see `SUPPORT.md \u003chttps://github.com/ome/omero-iviewer/blob/master/SUPPORT.md\u003e`_\n\nRequirements\n============\n\n* OMERO 5.6.0 or newer.\n\nInstall\n=======\n\nInstructions on how to add the OMERO.iviewer app to your installed OMERO.web apps\ncan be found in the `OMERO.iviewer README \u003cplugin/omero_iviewer/README.rst\u003e`_.\n\nUsage\n=====\n\nA guide to using OMERO.iviewer can be found on\nhttps://omero-guides.readthedocs.io/en/latest/iviewer/docs/index.html\n\nSettings\n========\n\nSee the `OMERO.iviewer settings \u003chttps://github.com/ome/omero-iviewer/blob/settings_docs/docs/settings.md\u003e`_\nfor details on how to configure various settings.\n\nKnown issues\n============\n\nFor images with many channels (greater than approximately 30 channels), saving\nof rendering settings fails due to the length of the request string. See\n`#321 \u003chttps://github.com/ome/omero-iviewer/issues/321\u003e`_. A work-around is to\nconfigure gunicorn to allow longer request strings. For example, to double the\nallowed limit::\n\n    omero config set omero.web.wsgi_args ' --limit-request-line 8192'\n\nWhen a palette is defined it will try to use the first value as the default ROI color.\nCurrently only rgb() vals are correctly parsed. If you try to use hex or a css name it will default to black\nYou can look up a conversion to rgb and set that as your first value for a workaround\n\nSupported URLs\n==============\n\nIf you have configured OMERO.iviewer as your default viewer (see install) then\ndouble-clicking an Image in OMERO.web will open OMERO.iviewer as the OMERO.web viewer, passing the current Dataset if the Image is in a Dataset::\n\n    /webclient/img_detail/1/?dataset=2\n\nYou use the OMERO.webclient's 'Open with...' menu to open multiple selected Images\nor a Dataset or a Well in OMERO.iviewer directly::\n\n    /iviewer/?images=1,2,3\n    /iviewer/?dataset=4\n    /iviewer/?well=5\n\nOther query parameters can be used to set the rendering settings for the\nfirst image, including channels in the form of ``index|start:end$color``::\n\n    ?c=1|100:600$00FF00,-2|0:1500$FF0000      # Channel -2 is off\n\nYou can also specify the rendering Model (greyscale or color) and\nZ-Projection (maximum intensity or normal)::\n\n    ?m=g            # g for greyscale, c for color\n    ?p=intmax       # intmax for Maximum intensity projection, normal for no projection\n\nThe Z and/or T plane, X/Y center position and zoom can be defined by::\n\n    ?z=10\u0026t=20          # can use z or t on their own\n    ?x=500\u0026y=400        # need to specify center with x AND y\n    ?zm=100             # percent\n\nYou can set the left and right panels to be initially collapsed::\n\n    ?collapse_left=true     # Left panel will be collapsed\n    ?collapse_right=true    # Right panel will be collapsed\n    ?full_page=true         # Both panels will be collapsed\n\n\nDevelopment\n===========\n\nIn order to run and build you need:\n\n* ``nodejs`` version at least 10.13.0 - https://nodejs.org/en/download\n* ``apache ant`` for css compiling and tests\n\nTo install node dependencies and build the JavaScript bundle:\n\n::\n\n    $ cd omero-iviewer\n    $ npm install\n\n    # uncompressed build\n    $ npm run debug\n\n    # OR compressed for production\n    $ npm run prod\n\n\nYou will usually want to have OMERO.iviewer installed on a local omero-web server,\nto test the JavaScript built above. NB: first uninstall OMERO.iviewer if already installed,\nthen:\n\n::\n\n    $ cd plugin\n    $ pip install -e .\n\n    # config\n    $ omero config append omero.web.apps '\"omero_iviewer\"'\n    $ omero config set omero.web.viewer.view omero_iviewer.views.index\n\nNow you can open Images from the webclient as normal.\n\n\nFor iterative development, it is recommended to use the webpack dev-server to build and serve OMERO.iviewer\nas this will re-compile automatically when files are saved.\n\nThe dev build of OMERO.iviewer will attempt to connect to a local OMERO server at http://127.0.0.1:4080.\nThe web server at this location will need to have CORS enabled and you should\nlogin to the webclient there.\n\nThe OMERO.iviewer will try to open an Image or other data from your local server, using IDs specified\nin `index-dev.html \u003csrc/index-dev.html\u003e`_:\n\n.. code-block:: html\n\n    \u003chtml\u003e\n        \u003chead\u003e\n            \u003clink rel=\"stylesheet\" type=\"text/css\" href=\"build/css/all.min.css\" /\u003e\n\n            \u003cscript type=\"text/javascript\"\u003e\n                // modify according to your needs\n                // in particular: choose an existing id !\n                window.INITIAL_REQUEST_PARAMS = {\n                        'VERSION': \"DEV_SERVER\",\n                        'WEB_API_BASE': 'api/v0/',\n                        'IMAGES': \"12345\",\n                        // 'DATASET': \"1\",\n                        //'WELL': \"1\"\n                };\n            \u003c/script\u003e\n    ...\n\nEdit the `IMAGES` ID in that file and save, then start the dev server:\n\n::\n\n    $ npm run dev\n\n\nTo connect to an omero-web server at a different URL or port, you will need to modify all\nproxy target entries in `webpack.dev.config.js \u003cwebpack.dev.config.js\u003e`_:\n\n.. code-block::\n\n    devServer: {\n        proxy: {\n            '/iviewer/**': {\n                target: 'http://localhost:your_port'\n            },\n            '/api/**': {\n                target: 'http://localhost:your_port'\n            }, ...\n        }\n    }\n\nIf you want to bind the webpack dev server to a port other than 8080\nyou will need to change its port property in `webpack.dev.config.js \u003cwebpack.dev.config.js\u003e`_:\n\n.. code-block::\n\n    devServer: {\n        port: your_port\n    }\n\nTesting\n=======\n\nTo run all tests, run:\n\n::\n\n    $ ant unit-tests\n\nFor more details on testing, see https://github.com/ome/omero-iviewer/tree/master/tests\n\nDocumentation\n=============\n\nA high-level description of the OMERO.iviewer application can be found at\nhttps://github.com/ome/omero-iviewer/tree/master/docs.\n\nTo build the JavaScript code documentation in build/docs, run:\n\n::\n\n    $ npm run docs\n\nol3-viewer\n==========\n\nThe OMERO.iviewer's internal image viewer is based on `OpenLayers \u003chttps://openlayers.org/\u003e`_,\n\nFor details on how to run and test this viewer independently of the OMERO.iviewer,\nsee https://github.com/ome/omero-iviewer/tree/master/plugin/ol3-viewer\n\nMore details\n============\n\nMore detailed resources on how to create a web app and development setup can be found at:\n\n1. `CreateApp \u003chttps://docs.openmicroscopy.org/latest/omero/developers/Web/CreateApp.html\u003e`_\n2. `Deployment \u003chttps://docs.openmicroscopy.org/latest/omero/developers/Web/Deployment.html\u003e`_\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fome%2Fomero-iviewer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fome%2Fomero-iviewer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fome%2Fomero-iviewer/lists"}