Open Microscopy Environment

Hi,
Does anyone have any software recommendations for volume viewing of confocal z stacks stored in OMERO? OMERO itself does a great job with plane views but working through the obvious candidates a quick google throws up I haven't been able to find anything that's happy with ome-tiff and will render well. I'd like something that was callable from the client (ideally visualisation via a web plugin but I don't think thats an option).
Thanks in advance for any suggestions.
Andy

Hi,

The OMERO.web has a limited ability to view some volumes (see http://www.openmicroscopy.org/site/prod ... -omero.web) but this is not really designed for confocal images.

We have experimented with providing an orthogonal view of a Z stack (both in the web http://trac.openmicroscopy.org.uk/ome/r ... Viewer.mov and OMERO.insight) but I guess that's not what you're after.

If you want a "true" volume viewer client for OMERO, you should have a look at the "Volviewer" from the John Innes center http://cmpdartsvr3.cmp.uea.ac.uk/wiki/B ... /VolViewer. This has been built as an OMERO client, although I don't think the downloads provided above have the OMERO client functionality. If you're interested in using this as an OMERO client, let us know (also which version of OMERO you're using and what OS+version you want to use this on) and we'll see what the current status of this is.

I also believe that various ImageJ plugins provide some 3D viewing options, although you'd need to investigate this yourself. We provide an ImageJ plugin for OMERO, so you can open images in ImageJ and if you find 3D plugins that work for you, then this could be a valid option.

Cheers,

Will.

Hi Will,
Thanks for the info. As you say the movie showing the orthogonal viewer isn't quite what I was after, although if it was implemented I would find it a useful addition. Is it planned to add it to future OMERO builds?

I'd already tried to get Volviewer to work (Windows 7x64 ) but the OMERO integration fails and opening ome-tiff's directly caused a CTD so I hadn't pursued further. If you had any info on stability updates etc that would be useful as it appears to be exactly what I'm after.(the OMERO server is 4.4 running on Ubuntu 12.04, insight clients would be on windows 7, possibly MacOSX) If I at least know it should work I could put some additional time into troubleshooting.

I'd also already tried the imageJ integration which again works well with just planes but the available plugins for 3D visualisation were unstable.

Thanks
Andy

Hi Andy,

what versions/builds of OMERO and VolViewer are you using?

Cheers,
~Josh.

Hi Josh,
Volviewer is v3.0 rev234, OMERO is 4.4.4-ice35-b3099.
Thanks
Andy

Hi Andy,

sorry for the long wait. I don't know what would be keeping 4.4.4 from working. Do you have a log or similar of the error you are seeing?

~Josh

Hi Josh,
Using the open with option for Volviewer from within Insight client I get 'Object ready to be opened' in the OMERO activities interface. Then a command prompt window for Volviewer pops up which goes through loading with no errors shown, just a comment that double precision constant is represented as single. The Volviewer application then opens but with no file loaded.
If I open Volviewer separately and try to use the OMERO import option I get a runtime error for the Volviewer.exe , in a window labelled Visual C++ Runtime library, 'this application has requested the runtime to terminate it in an unusual way'. This occurs after 'OMERO:creating session' In the Volviewer command prompt window.
Event viewer Admin event log shows this as Event 1000 Application error see below.
Thanks
Andy

Faulting application name: VolViewer.exe, version: 0.0.0.0, time stamp: 0x4fbfa18c
Faulting module name: MSVCR90.dll, version: 9.0.30729.6161, time stamp: 0x4dace4e7
Exception code: 0x40000015
Fault offset: 0x0000000000042686
Faulting process id: 0x1c30
Faulting application start time: 0x01cdf4c5621194b6
Faulting application path: C:\Program Files\VolViewer\VolViewer.exe
Faulting module path: C:\Windows\WinSxS\amd64_microsoft.vc90.crt_1fc8b3b9a1e18e3b_9.0.30729.6161_none_08e61857a83bc251\MSVCR90.dll
Report Id: 2f4c616e-60b9-11e2-b5dd-782bcbb1e008

I also had a go at running Volviewer on my home machine and got the same error on trying to use the omero import option. In this case there were no additional comments as Volviewer loaded.
An additional note in the Volviewer window as the error occured was 'Qt has caught an exception thrown from an event handler. throwing exceptions from an event handler is not supported in Qt. You must reimplement QApplication ::notify() and catch all exceptions there.
Cheers
Andy

Hi Andy,

Could you also provide the debug / verbose console output from VolViewer during that error?

Thanks,
~Josh.

Hi Josh,
Do you know how to switch on debug/verbose?
Thanks
Andy