Open Microscopy Environment

Hi OME team,

I'm running into problems with data from a Zeiss 780 when users take multiple XY positions. The Zen software saves a single lsm file with all the XY stacks.

When uploading into OMERO, the XY points are successfully separated into the images but the stacks are mangled, with wrong frames in the stack or a portion of one channel in the wrong place.

This also happens in Fiji, with and without SCIFIO (which doesn't recognise the multiple XY positions). The closest I have come is to turn off SCIFIO, then open the stack with ImageJ (IE NOT bioformats) which gives me a concatenated stack that still has a few disrupted images (the first few images of each stack except the first one).

Happy to upload an example (~4.5GB). Any thoughts appreciated as always.

Best,

Dave Mason

Hi Dave,

Which version of Bio-Formats/OMERO are you using? If you see this problem with 5.0.2, then it would be helpful to have an example file - I will send information on how to upload the file in a private message.

Regards,
-Melissa

Hi Melissa,

Thanks for the quick reply, my server is OMERO 5.0.2-ice34-b26 and I'm using Fiji running 5.0.2-DEV (revision 607705e).

I'm in the process of uploading a data set and will be interested to see what you make of it.

Thanks,

Dave

Hi Dave,

Thank you very much for uploading a dataset. We now have a proposed fix:

https://github.com/openmicroscopy/bioformats/pull/1210

I would expect that to be included in the upcoming 5.0.3 release of Bio-Formats/OMERO.

Regards,
-Melissa

Melissa;

Thanks for looking into that. Quick question;

If the fix is incorporated and I update the OMERO server to 5.0.3 in August, will data already uploaded then open correctly? I'm not sure whether bioformats comes into play every time an image is opened or only upon upload.

Presumably the thumbnails will remain incorrect as they're created upon upload. If there someway to refresh the thumbnails other than deleting and re-uploading the data?

Thanks,

Dave

Hi Dave,

If the fix is incorporated and I update the OMERO server to 5.0.3 in August, will data already uploaded then open correctly? I'm not sure whether bioformats comes into play every time an image is opened or only upon upload.

Files that have already been uploaded should open correctly without needing to be reimported.

Presumably the thumbnails will remain incorrect as they're created upon upload. If there someway to refresh the thumbnails other than deleting and re-uploading the data?

The easiest way I can think of is to right-click the image in Insight, and select "Rendering Settings > Reset and Save". Right-clicking the name of the image in left-hand tree in OMERO.web and selecting "Rendering Settings > Set Owner's" may have a similar effect, though someone else may have an idea of a more efficient way to do that.

-Melissa