omero-iviewer 0.17.0

A Python plugin for OMERO.web

OMERO.iviewer

An OMERO.web app for visualizing images in OMERO.

Requirements

• OMERO 5.6.0 or newer.

Installing from PyPI

This section assumes that an OMERO.web is already installed.

Install the app using pip:

NB: You need to ensure that you are running pip from the python environment where omero-web is installed. Depending on your install, you may need to call pip with, for example: /path/to/venv/bin/pip install ...

$ pip install -U omero-iviewer

Add iviewer custom app to your installed web apps:

$ omero config append omero.web.apps '"omero_iviewer"'

To replace the default omero.web viewer:

$ omero config set omero.web.viewer.view omero_iviewer.views.index

To enable the “open with” feature:

$ omero config append omero.web.open_with '["omero_iviewer", "omero_iviewer_index",
  {"supported_objects":["images", "dataset", "well"],
   "script_url": "omero_iviewer/openwith.js", "label": "OMERO.iviewer"}]'

If you want to redirect /iviewer/ URLs to instead use /webclient/img_detail/ID so that a different viewer configured at omero.web.viewer.view is used then use the config below. This will redirect /iviewer/?images=12,34 to /webclient/img_detail/12/?images=12,34, /iviewer/?roi=56 to /webclient/img_detail/IMAGE_ID/?roi=56 (same for shape) and /iviewer/?well=78 to /webclient/img_detail/IMAGE_ID/?images=ID1,ID2,... where ID1, ID2, etc are the images in the well.

$ omero config set omero.web.iviewer.redirect_iviewer True

Now restart OMERO.web as normal.

Usage

A guide to using OMERO.iviewer can be found on https://omero-guides.readthedocs.io/en/latest/iviewer/docs/iviewer.html

License

OMERO.iviewer is released under the AGPL.

Copyright

2017-2022, The Open Microscopy Environment