An OMERO.web app for visualizing images in OMERO.
Also see SUPPORT.md
- OMERO 5.6.0 or newer.
Instructions on how to add the OMERO.iviewer app to your installed OMERO.web apps can be found in the OMERO.iviewer README.
A guide to using OMERO.iviewer can be found on https://omero-guides.readthedocs.io/en/latest/iviewer/docs/index.html
See the OMERO.iviewer settings for details on how to configure various settings.
For images with many channels (greater than approximately 30 channels), saving of rendering settings fails due to the length of the request string. See #321. A work-around is to configure gunicorn to allow longer request strings. For example, to double the allowed limit:
omero config set omero.web.wsgi_args ' --limit-request-line 8192'
When a palette is defined it will try to use the first value as the default ROI color. Currently only rgb() vals are correctly parsed. If you try to use hex or a css name it will default to black You can look up a conversion to rgb and set that as your first value for a workaround
If you have configured OMERO.iviewer as your default viewer (see install) then double-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:
/webclient/img_detail/1/?dataset=2
You use the OMERO.webclient's 'Open with...' menu to open multiple selected Images or a Dataset or a Well in OMERO.iviewer directly:
/iviewer/?images=1,2,3 /iviewer/?dataset=4 /iviewer/?well=5
Other query parameters can be used to set the rendering settings for the
first image, including channels in the form of index|start:end$color:
?c=1|100:600$00FF00,-2|0:1500$FF0000 # Channel -2 is off
You can also specify the rendering Model (greyscale or color) and Z-Projection (maximum intensity or normal):
?m=g # g for greyscale, c for color ?p=intmax # intmax for Maximum intensity projection, normal for no projection
The Z and/or T plane, X/Y center position and zoom can be defined by:
?z=10&t=20 # can use z or t on their own ?x=500&y=400 # need to specify center with x AND y ?zm=100 # percent
You can set the left and right panels to be initially collapsed:
?collapse_left=true # Left panel will be collapsed ?collapse_right=true # Right panel will be collapsed ?full_page=true # Both panels will be collapsed
In order to run and build you need:
nodejsversion at least 10.13.0 - https://nodejs.org/en/downloadapache antfor css compiling and tests
To install node dependencies and build the JavaScript bundle:
$ cd omero-iviewer $ npm install # uncompressed build $ npm run debug # OR compressed for production $ npm run prod
You will usually want to have OMERO.iviewer installed on a local omero-web server, to test the JavaScript built above. NB: first uninstall OMERO.iviewer if already installed, then:
$ cd plugin $ pip install -e . # config $ omero config append omero.web.apps '"omero_iviewer"' $ omero config set omero.web.viewer.view omero_iviewer.views.index
Now you can open Images from the webclient as normal.
For iterative development, it is recommended to use the webpack dev-server to build and serve OMERO.iviewer as this will re-compile automatically when files are saved.
The dev build of OMERO.iviewer will attempt to connect to a local OMERO server at http://127.0.0.1:4080. The web server at this location will need to have CORS enabled and you should login to the webclient there.
The OMERO.iviewer will try to open an Image or other data from your local server, using IDs specified in index-dev.html:
<html>
<head>
<link rel="stylesheet" type="text/css" href="build/css/all.min.css" />
<script type="text/javascript">
// modify according to your needs
// in particular: choose an existing id !
window.INITIAL_REQUEST_PARAMS = {
'VERSION': "DEV_SERVER",
'WEB_API_BASE': 'api/v0/',
'IMAGES': "12345",
// 'DATASET': "1",
//'WELL': "1"
};
</script>
...Edit the IMAGES ID in that file and save, then start the dev server:
$ npm run dev
To connect to an omero-web server at a different URL or port, you will need to modify all proxy target entries in webpack.dev.config.js:
devServer: {
proxy: {
'/iviewer/**': {
target: 'http://localhost:your_port'
},
'/api/**': {
target: 'http://localhost:your_port'
}, ...
}
}
If you want to bind the webpack dev server to a port other than 8080 you will need to change its port property in webpack.dev.config.js:
devServer: {
port: your_port
}
To run all tests, run:
$ ant unit-tests
For more details on testing, see https://github.com/ome/omero-iviewer/tree/master/tests
A high-level description of the OMERO.iviewer application can be found at https://github.com/ome/omero-iviewer/tree/master/docs.
To build the JavaScript code documentation in build/docs, run:
$ npm run docs
The OMERO.iviewer's internal image viewer is based on OpenLayers,
For details on how to run and test this viewer independently of the OMERO.iviewer, see https://github.com/ome/omero-iviewer/tree/master/plugin/ol3-viewer
More detailed resources on how to create a web app and development setup can be found at: