Open Microscopy Environment

Hello,

I have a few folders within Omero where the images are not displayed as thumbnails but instead a yellow clock icon is visible. The files uploaded fine, with no error messages.

Within the folder/workspace, some of the files are dm3 and some are tif but there does not seem to be a correlation between the file type and this display error. I can open the files directly from my hard drive so the files are not corrupt. Of the images which are not yellow clock icons in the workspace view, the dm3 files are displayed as b/w pixels and the tif images are displayed as true thumbnails

I have also attached a screenshot of the workspace. If I close omero and re-open it, it is not always the same files that appear as a clock.

I tried deleting the folder within omero and uploading the images again, same problem. I have logged in to omero from a mac and a PC, same issue.

Can anyone shed some light on this please?!

Sam

Hi Sam,

I'm going to assume that these are "big" images (over approx 3k * 3k pixels) and that you're seeing the "timer" icon while OMERO generates a pyramid of different resolution tiles to enable tiled image viewing.
Pyramid generation will take various lengths of time, depending on the size of the images and your server spec but can be many hours for very large images. If you periodically refresh the thumbnails you should see more of them complete, to show the finished thumbnail which indicates that the image is ready to view.

If these are not "big" images or some of them fail to complete then let us know.

I don't know what the issue is with the pixellated dm3 thumbnails. Are these "big" images? Do they open OK in the full viewer or "Preview" tab?
If you want us to have a look at them and investigate the problem, you can upload files at https://www.openmicroscopy.org/qa2/qa/upload/

Regards,

Will.

Thanks for your response

You are right about the size being the issue, the ratio of clocks to real thumbnails is decreasing.

Yes, the dm3 files are big images (4k*4k) but I expected them to be displayed eventually like the large tif files. It is not the end of the world but its a pain to not be able to directly store dm3 or dm4 files on omero.

Sam

Hi Sam,

OMERO certainly should work fine with dm3 files, so if you have a sample for us to work with we can try and fix any issues with it (see upload link above).

I don't think OMERO supports dm4, but if it's a format you want to work with, we'd be happy to try and support it. Again, if you could let us have a sample file we can work with that would be great.

Regards,

Will.

Hi,

I would like to retake this post because I am having similar problems.

I uploaded images from our high-content screen microscope and I cannot see the thumbnails on the workspace.

Additionally, when using the web application the images don't load in the viewer. If I use the insight application, then they do after double clicking.

The images are 16bit, 8mb on size and 2048x2048 pixels, nothing spectacular.

Any ideas or suggestions?

Thanks a lot in advance!

Hi Jordi,

Could you tell us what version of omero server and insight you are using?

Also, it would be really helpful if you could let us have a sample file to test with (you can upload a file via https://www.openmicroscopy.org/qa2/qa/upload/)

Thanks,
Riad

Hi Riad,

Thanks for your reply.

I think that we are using this version in the server but I'm not sure (I'm not the owner) OMERO.web 5.4.7-ice36-b93.

As for the Insight, I use this version 5.4.9-ice36-b101.

I have uploaded both examples images and also the system file of our microscope with file extension .xdce

Thanks!

Best,

Jordi

PS: for whatever reason the user name or my e-mail was not registered, please see the screenshot for the ID of my upload.

Dear Jordi,

Thank you for the version information. Just to check, what permissions are on the group that the images are in? Is it read-only?

Who's doing the importing and who's trying to view them? The actual OMERO owner of the images, some administrator, etc.?

Cheers,
Mark

Hi Mark,

We have Read-Annotate permissions (rwra--) in the group.

We are, including me, whom is now testing the system, Members of the group, but not Owners, does that make a difference?

Thanks!

Best,

Jordi

Hi again,

I actually tried the5.4.7-ice36-b93 version of Insight and the thumbnails are now displayed, if I try the b101 version, they are not...

Still, nowhere to be seen in the web version :/

Thanks!

Best,

Jordi

PS: I have put myself as Owner as well, and it didn't make any difference.