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OMERO.autotag

OMERO.autotag is a plugin for OMERO.web that automates the application of tags to images based on the original filename, path, and extensions of the images.

This was formerly part of OMERO.webtagging, the umbrella name for tools developed to enhance use of text annotations (tags) in OMERO.

Requirements

As Python 2 has now reached end-of-life, OMERO 5.6 now requires Python 3. With release 3.1.0 of autotag, the following are now required. To use autotag on older OMERO systems (running Python 2), please use versions older than 3.1.0.

  • Python 3.8 or later
  • omero-web 5.6 or later
  • django 4.2 or later

User Documentation

http://help.openmicroscopy.org/web-tagging.html

Installation

The recommended way to install autotag is using pip, but it is also possible to install it manually as described here.

# In the python environment of OMERO.web (virtualenv or global)
pip install omero-autotag

# Add autotag to webclient
omero config append omero.web.apps '"omero_autotag"'

# Add autotag to centre panel
omero config append omero.web.ui.center_plugins '["Auto Tag", "omero_autotag/auto_tag_init.js.html", "auto_tag_panel"]'

Upgrade from omero-webtagging-autotag to omero-autotag

Since 3.2.2, the package was renamed to omero-autotag. This is a breaking change for OMERO.web, as the old package must be removed from the OMERO.web config and replaced by the new package.

You can perform the upgrade as follow:

# stop omero web
# Install the new package and uninstall the old one
pip uninstall omero-webtagging-autotag
pip install omero-autotag

# Then open the OMERO.web configuration editor
omero config edit
# Update the two configurations called 'omero.web.apps' and 'omero.web.ui.center_plugins'
# In 'omero.web.apps': 'omero_webtagging_autotag' -> 'omero_autotag'
# In 'omero.web.ui.center_plugins': '["Auto Tag", "omero_webtagging_autotag/auto_tag_init.js.html", "auto_tag_panel"]' -> '["Auto Tag", "omero_autotag/auto_tag_init.js.html", "auto_tag_panel"]'
# start omero web

Note that installing the latest omero-webtagging-autotag is not functional but has a dependency on omero-autotag. Thus, if you wish to use the old version omero-webtagging-autotag, make sure to specify the latest working version:

# ONLY IF YOU WANT TO USE AN OLDER VERSION OF THE PLUGIN
# stop omero web
pip install omero-webtagging-autotag==3.2.0
# And set the configuration accordingly
# start omero web

Documentation

Available on the OMERO website.

Development

Uses node and webpack.

This will detect changes and rebuild static/autotag/js/bundle.js when there are any. This works in conjunction with django development server as that will be monitoring bundle.js for any changes.

To build the node components on changes

cd omero_webtagging_autotag
npm install
node_modules/webpack/bin/webpack.js --watch

To install using pip in development mode (in appropriate virtualenv)

# In the top-level autotag directory containing setup.py
pip install -e .
cd $OMERO_PREFIX

OMERO development server can then be started in the usual way. Remember to configure the autotag settings the same as above.

Project Maintenance

I (Douglas) am no longer actively developing OMERO.webtagging. I am thrilled to hand over maintainence and development to German Bioimaging.

Acknowledgements

OMERO.webtagging was created by Douglas P. W. Russell ([email protected]) while at Oxford University and Harvard Medical School, then later extended by DPWR Consulting Ltd.

These plugins were developed originally with the support of Micron Advanced Bioimaging Unit funded by the Wellcome Trust Strategic Award 091911, and Open Microscopy.

Continued development was supported by The Laboratory of Systems Pharmacology, Harvard Medical School and Research Computing, Harvard Medical School.

Continued development was sponsored by Micron Advanced Bioimaging Unit funded by the Wellcome Trust Strategic Award 107457.