Some imported images are distorted in OMERO

I imported jp2 files taken with Stereo Investigator software and found that some images are distorted obliquely. In some cases, the image in full view is normal but only the thumbnal is distorted.

Is this a known issue?

It could be that the image files may have their own problems, but they look normal in Stereo Investigator or in ImageJ/Fiji.

I’m happy to send you the image files if you need them.

Hi,

Yes please, a sample file(s) would be very helpful.
Please upload at https://www.openmicroscopy.org/qa2/qa/upload/

When the images look “normal” in Fiji, are you opening them via the BioFormats plugin or some other way?

Thanks,
Will.

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Flash will be frozen in December. Maybe you need a new tool?

When the images look “normal” in Fiji, are you opening them via the BioFormats plugin or some other way?

Yes, I used Fiji and Bio-Formats importer.

Sorry for the trouble. Do you still have the information for uploading FTP that we provided previously? If so, please use that and let us know when the transfer is not. If not, I’ll re-send.

Don’t we know it. Thanks for the prompting. We spent some time discussing during today’s community meeting and will try to resurrect a previous attempt to bury Flash.

All the best,
~Josh

Can you resend the details, please?

@kouichi-c-nakamura,

Sent via email.

~Josh

Hi Kouichi,

sorry for the delay and thanks for uploading the file. I have imported it into one of our test servers and the image seems to read as expected. At least no visible distortion appears either in the viewer panel or in the generated thumbnail:

Which version of OMERO.server and OMERO.web are installed in the deployment where you are seeing this rendering issue? Could you independently try importing an image failing on your side into the OMERO demo server which is running the latest released version of the software to confirm the issue is not present there?

Best,
Sebastien

Thanks for the reply.

Starting with the easiest answer, OMERO.web is 5.6.3.

We haven’t managed to update our OMERO and the problem remains. I noticed that in some cases, not all, the distortion is dependent on zoom size. In the example below, while 17% zoom looks fine, 15% zoom shows the distortion. Does this ring any bell?

Hi Kouichi,

We were wondering whether this was to rather meant be interpreted as “we managed to update our OMERO and the problem remains.”. In all cases, could you confirm the current version of OMERO.server (as I suspect the issue might lie at the level of Bio-Formats)?

We will try to get back to you on this issue although at the moment, we are dealing with all our UoD systems including all our testing infrastructure being down following a power outage so please bear with us.

No, we haven’t managed, although I wish we have. We’re being slow about this these days…

Server version is “most likely” 5.6.1.

Hi Kouichi,

now most systems are back, I finally get to test the sample file already tested in Some imported images are distorted in OMERO in an OMERO 5.6.1 server and I have the same result as above i.e. I cannot detect any distortion at any zoom level.

One thought: were the distorted image recently imported or are were they imported under previous server versions?

Best,
Sebastien

1 Like

Thanks for testing.

We haven’t updated the OMERO server since March. The import was done recently with the same version (most likely 5.6.1). Mmm, I thought the older version was the issue.