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.
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.
NOTE: The original readme of this repository moved here.
A short tutorial on its usage in combination with the omero.forms plugin was posted here .