OMERO.iviewer: Failed to get image data

Hi,

I’d like to resurrect a topic from the old forum about an issue with opening Nikon .nd2 files in OMERO.iviewer.

After some more testing we are experiencing the error for nd2 files that have multiple Z-stacks and a single channel - single Z,C and multi Z,C open fine. This occurs for images from an A1 confocal and a Ti wide field.

We are going to the being patching out server this week and upgrading to the latest version of OMERO.iviewer so it would be good chance to work on this. Hopefully the issue resolves itself on patching/upgrading, but it would be great help if anyone has suggestions of components to check, logs to inspect or settings to tweak.

Thanks,

Chris

Hi Chris

Looking back at the old issue it doens’t look like we figured out the problem. You could retrying what was already discussed to see if any of the output has changed.

If you still have a problem could you give us as much information as possible on how you setup OMERO.server and OMERO.web, things like which set of instructions you followed, configs, operating system, how you’re starting OMERO, any customisations, etc.

Hi,

I’m waiting on the IT team to get back with details, but here’s a cartoon of setup:

PastedGraphic-1

Could be be some json santising by the firewall that sits between web and server?

Cheers,

Chris

Hi Chris,

Apologies for the delay.
One thing you could try to investigate this is to run OMERO.web via Docker, as an Internal user connecting directly to your OMERO.server without the Firewall (similar to Insight in your diagram).

This is relatively easy to try once you have docker available:

host=your.omero.server
docker run -it --rm -e OMEROHOST=$host -p 4080:4080 -v $appdir:$docker_appdir -v $config:$docker_config openmicroscopy/omero-web-standalone

Then open your browser at localhost:4080 and you should have webclient with iviewer etc connecting to the OMERO server you specified.

I expect this will “just work” and might not tell you much, but if it works from outside your data centre, then maybe you could try it from inside, connecting to OMERO via the Firewall?

Regards,

Will

Hi,

I was hoping after that after moving to a new server and upgrading to the 5.6.3 that this issue might resolve itself. However, we are get the error "parser error " opening multi-FoV Nikon files with OMERO.iviewer.

Screen Shot 2020-04-27 at 1.26.23 pm

Image viewer and OMERO.figure open these fine.

Any suggestions for where to start debugging?

Thanks,

Chris

Hi Chris,

Sorry to hear this long-running issue is still causing problems.

I seem to remember that our previous investigations suggested that it was the pixel size metadata that looks suspicious in the imageData JSON that iviewer was loading.

It’s interesting that this only affects some of your nd2 files. I know you have provided us with a sample file in the past but I wonder if you could upload a pair of “control (multi Z,C)” vv “failing (multi Z, single C)” images?

Also, I wonder if you’d be able to try my “docker” suggestion above, which might give us a clue.

Thanks,

Will

Hi Will,

thanks for the help on this one. I ran the docker as you suggested and everything works as you expected.

Attached is a screen shot of slide-by-side our server and local docker OMERO.web, this time for a Zeiss czi image.

Where do you want me upload examples to?

Thanks,

Chris

Hi Chris,
So that seems to confirm it’s the firewall that’s causing the problems. How the firewall is causing the JSON to become invalid with some characters is beyond my knowledge although others on the team (away just now) might have a clue. Any more info on the firewall might help here.

Could you upload the files at https://www.openmicroscopy.org/qa2/qa/upload/ (I’m afraid you’ll need to enable Flash since we’re still using a Flash-based uploader).
If you have a “failing” file and a very similar file that is “working”, that would be most useful.

Thanks,
Will.

Hi Will,

Thanks so much for all your work on this. I’ve arranged for our IT to look into this on Monday, so I’ll let know what happened.

After moving to 5.6 we now have production and development servers which are identical - previously they had a different setup.

The files open on dev, but not production. The only difference we are aware of is that they’re on different subnets.

Thanks,

Chris

Hi Will,

a quick update, it looks like F5 is the culprit. It sounds like it uses a non-spec conforming JSON parser:
https://support.f5.com/csp/article/K58055038

Cheers,

Chris

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Hi Chris,
Great that you found the solution (or at least the cause of the problem).

Will.