Previously, we used Fiji (Bio-Formats plugin) to extract metadata from TIFF files and then manually enter those values into openBIS.
Now we would like to do this directly in openBIS. When a user uploads a TIFF file via the GUI upload button, or when a file is ingested via a dropbox, openBIS should automatically read the metadata from the file and fill the corresponding sample or data set properties.
Is this possible in openBIS?
Should this be done using a dropbox script (Jython)?
Is there a way to support both GUI upload and dropbox, ideally reusing the same logic?
This is possible using openBIS dropbox scripts (Jython). We implemented something like this in the past to extract TIFF metadata from Scanning Electron Microscopy images during ingestion.
However, we no longer support dropbox-based solutions. That said, our old implementation is still available and might be helpful as a reference.
It shows how metadata can be read and mapped to data set properties.
Thank you very much for the information and for sharing your experience and the reference implementation .
Since dropbox-based solutions are no longer supported, I wanted to ask if there is any recommended alternative approach in openBIS today for extracting metadata during ingestion and mapping it to dataset properties.
Any guidance on the current best practice would be greatly appreciated.