Open Microscopy Environment

Hi Guys,

I am running latest 5.3.3 OMERO server and have had problems with JP2000 images (.jp2). The file has imported correctly and can be exported and opened. But within the database it does not generate a pyramid and gives the standard error message that "pyramid is being generated come back later". This never resolves. I have also tried converting the image to .jpf, same result. Mark

Image Details

Import Date: 2017-06-09 03:08:16
Dimensions (XY): 10277 x 19538
Pixels Type: uint8
Pixels Size (XYZ) (µm): -
Z-sections/Timepoints: 1 x 1
Channels: Red, Green, Blue
ROI Count: 0

Dear Mark,

Would it be possible to upload a copy of the image using http://qa.openmicroscopy.org.uk/qa/upload/ so we could take a closer look at it?

Thanks,
Roger

Hi there, I have just uploaded 2 JP2000 images which have imported but not generated either thumbnail or pyramid. cheers Mark

Image File

N365_296.j2k

20170607-Lamars-TestImage.jp2

Dear Mark,

Does your server's PixelData-0.log record a "java.lang.OutOfMemoryError" in response to these imports? I wonder if the problem is simply that of the pixel data thread running out of Java heap space. If so, https://docs.openmicroscopy.org/omero/5 ... y-settings may offer some workaround. Otherwise, it may be best if you could zip up your server logs and submit them to http://qa.openmicroscopy.org.uk/qa/upload/ with a note saying when one of the problematic imports occurred.

Cheers,
Mark