Open Microscopy Environment

Hello everyone,

I contact you because I have a problem to import large images in jpg format.

I imported images (jpg format) that have a resolution close to:
Dimensions (XY): 2592 x 3872 uint8
Dimensions (XY): 5472 x 3080 uint

These images are well converted into pyramid images and I can view them on omero.

but I have other images with dimensions (XY) 4800 x 3200 uint8, when I import them, the pyramid calculation time is very long and omero fails to transform it into a pyramidal image. I waited a whole day but a clock remains displayed.

thank you for your help

have a good day

sameh

Hi Sameh,

sameh wrote:but I have other images with dimensions (XY) 4800 x 3200 uint8, when I import them, the pyramid calculation time is very long and omero fails to transform it into a pyramidal image. I waited a whole day but a clock remains displayed.

Have you looked into the var/log/PixelsData-0.log ? Is the service running? Did it run out of memory? How much memory have you allocated?

See https://docs.openmicroscopy.org/omero/5.4.9/sysadmins/troubleshooting.html#outofmemoryerror-permgen-space-errors-in-omero-server-logs for more info.

~Josh

jmoore wrote:Hi Sameh,

sameh wrote:but I have other images with dimensions (XY) 4800 x 3200 uint8, when I import them, the pyramid calculation time is very long and omero fails to transform it into a pyramidal image. I waited a whole day but a clock remains displayed.

Have you looked into the var/log/PixelsData-0.log ? Is the service running? Did it run out of memory? How much memory have you allocated?

See https://docs.openmicroscopy.org/omero/5.4.9/sysadmins/troubleshooting.html#outofmemoryerror-permgen-space-errors-in-omero-server-logs for more info.


~Josh

Thanks a lot for your help.


we will check all memory settings before re-testing.


thank you so much

have a good day

sameh