/ometa

Community contributed scripts for metadata handling in omero-web

Primary LanguagePythonGNU General Public License v2.0GPL-2.0

ometa: contributed scripts for metadata handling in omero-web

Summary

This is the central repository for community contributed scripts to omero-web to support metadata handling and bulk annotation with key-value pairs. These scripts, in combination with the omero.forms, support the bulk annotation workflow described in this blog post.

Content

This repository provides five scripts:

  • 01-KeyVal_from_Description.py: Parses a Dataset/Project/Screen description and converts key:value pairs into map annotations in the same container.
  • 01-KeyVal_to_csv.py: Converts a dataset map annotation into a table with one record for every image in the dataset. Columns are named according to map annotation keys. The first column contains the image filename (or id???)
  • 03-KeyVal_from_csv.py: Parses a given csv table attachment and converts each record into a map annotation for the image identified via the entry in the first column (filename or image id).
  • 04-Remove_KeyVal.py: Removes all map annotations from a dataset and all contained images.
  • 05-KeyVal_from_Filename.py: Creates image map annotation by tokenizing the filename.

Installation

The scripts must be placed in the OMERODIR/lib/scripts/omero directory of your omero installation, preferrentially in a seperatate subdirectory, e.g. Bulk Annotation/.

OMERODIR refers to the root directory of you omero server. If you followed the installation procedures, you should have the $OMERODIR environment variable set. Logged in omero admins can also use the "Upload scripts" button in the Gears menu.

After installation, the scripts will be accessible in omero web by clicking the Gears icon in the menu bar.

History

This repository started as a fork of evehuis/omero-user-scripts. Ownership was transferred to @CFGrote after merging a pull request that fixed a number of bugs and ported the original code from python2.7 to python3.x

Contributions

Contributions are welcome: Bugfixes, enhancements, additional scripts, tests etc should be submitted as pull requests. We also encourage you to post suggestions or bug reports in our github issues.