Open Microscopy Environment

Hi

I am having an issue with files saved in Metamorph. Neither files saved as Metamorph tiff or stk are displayed in Omero. The Metamorph tiffs upload but aren't displayed properly and the stk files upload but I get a message from Insight telling the image is not valid when trying to use the image viewer. I have uploaded a tif and stk file to Omero.qa.

Cheers,

Dan.

Hi Dan,

Sorry to hear you're having a problem, and thanks for uploading the images for us to take a look at them.

Which version of OMERO are you using?

I have checked with the pending release 4.4 (.10) and 5.0 versions of Bio-Formats, and also back to 4.4.8 and all were able to read and display the two images (stk and tiff) you uploaded without trouble. I have then imported both images onto a 4.4. (.10) server and was able to view the images using both the Insight and web clients. In all cases, the images were shown as being 16 bit single channel greyscale, 512×512 pixels.

The upcoming OMERO 4.4.10 release does contain some metamorph bug fixes. I would suggest upgrading to 4.4.10 if you are using an earlier 4.4 release, when this is made available. This should be quite soon; we are testing a prerelease right now.


Regards,
Roger Leigh

Hi Roger

Thanks for taking a look for me. We are running Omero 5.0.0-beta1-ice34-b3470. How do I check which version of Bioformats is being used? Is it possible the Bioformats version is lagging behind in terms of bug fixes for this beta version of the server?

Cheers,

Dan.

Hi Dan,

If you're using beta1, that dates back to June and at that point may not have contained all the fixes which went into 4.4.8 around the same time. You might want to try the 5.0.0-rc1 release which was released just before Christmas: http://downloads.openmicroscopy.org/omero/5.0.0-rc1/ which contains all the changes and bugfixes since then. I just tried it with our current 5.0 build (not very different from the rc1 release), and your images import and view correctly, so it's quite likely the upgrade would fix this for you also.


Kind regards,
Roger

Hi Roger,

We'll give it a shot! Many thanks for the prompt reply!

Dan.