Open Microscopy Environment

OMERO cannot read MBF Stereo Investigator's customized jpeg 2000 images directly. At the moment, I need to export as TIFF or other format and then import to OMERO.

Bio-Formats can read it, so OMERO must be able to read it too.

I'm happy to send you an example image file if you need one.

Which versions of Bio-Formats and OMERO have you been using with these files?
If you have a sample file you can upload it to https://www.openmicroscopy.org/qa2/qa/upload/

I've uploaded the following file:

`000000_000034.jp2` from `20180703 GlyT2 VAChT\Gt VAChT Immunostar_10x\0001s` (my internal reference)

Bio-Formats for ImageJ is 5.9.0

OMERO.insgith is 5.4.6-ice36-87

Code: Select all

cs = session.getConfigService
cs.getVersion


returned

5.4.6

We received the upload QA file and I was able to test it with both Bio-Formats 5.9.0 and OMERO 5.4.6. In both cases the file was read without error and displayed the same using either method. What sort of error or problems have you seen when using OMERO?

Thank you for checking.

I tested it again with our OMERO server and you're right, it worked.

I also tested a much larger image stitched by StereoInvestigator (single channel) and it was fine.

I further tested a large stitched image with multiple colors and it was fine too.

I guess when I first tried many of those .jp2 files, our server might have been experiencing some kind of temporal error. It was only a few weeks ago, but however long I waited, I was never able to open the uploaded .jp2 files.

Now it seems perfectly fine. Thank you for your investigation.