Open Microscopy Environment

Hi,

I have been using the OMERO plugin for FIJI/ImageJ and i noticed that when i import the modified images back into OMERO from FIJI, using the 'save image(s) to OMERO' button, they are converted to OME.Tif's regardless of what their original format is.
Is this supposed to happen? and is there a way for me to import them back into OMERO maintaining their original format after they have been modified?
Thank you for your help.

Kind, Regards
Ben

Hi Ben,

Thank you for reporting your issue.

Yes you are right, the OMERO_IJ plugin exports all “modified/processed” images as ome.tif’s back to OMERO when you use the ‘save images(s) to OMERO’ option.The plugin uses Bio-Formats for writing files and currently, we have made the ome-tiff export as the default option for modified/processed images, but this can definitely be improved.

The file formats which can be written using Bio-Formats are listed in the following link,
https://www.openmicroscopy.org/site/sup ... riter.html

and we could maybe try and expose these options (export as tiff, png,jpeg,etc) in future cases (if that sounds like an useful option for the user community).

Best,
Balaji