I’m hoping to get some insight/suggestions for using bioformats2raw and raw2ometiff to convert 3DHISTECH MRXS files to OME-TIFF to be imported into Omero. I am a Sysadmin working to integrate/automate some processes and have very limited background in these imaging formats. I’ve done some reading starting here and the github repos & issues for both tools and generally have the process working, that’s not really the problem. The concern I have is the drastic increase in size from the MRXS to OME-TIFF.
I’m seeing anywhere from a 4x to 6x increase in size after conversion using JPEG-2000 compression on the OME-TIFF (the default LZW is obviously much larger yet). At first I thought maybe it was a problem with the source images due to our scanner settings, so I tried converting some examples from here with similar results.
At this point I have stuck to what seems like the common CLI options for the tools, here’s some examples of what I’m using:
bioformats2raw --resolutions=6 CMU-2.mrxs CMU-2_raw raw2ometiff --compression=JPEG-2000 CMU-2_raw CMU-2-JPEG-2000.ome.tiff
The above starts with ~1.3 GB at the source and results in ~7.1 GB OME-TIFF file. As our real world source images are anywhere from 10-30 GB usually, this is a concern.
Am I missing anything? Are there any other options that would help with the file size without noticeable quality loss? I’ve also seen this Github issue which is starting to lead me to believe this is expected and its not me doing something wrong.
Any insight is greatly appreciated, thanks!