Open Microscopy Environment

Hello everybody,
I'm using the omero demo server to validate, if omero might be a solution for our institute. We have often to deal with large large images (500 MB -1 GB). Uploading of the pictures on the server works like a charm. But when I try to open/view them, it fails - although smooth and easy work flow with large images is propagated on the omero web site. Has it something to do with the used omero server? Thank you in advance for any help.

Best regards,
Michael

Hi Michael,

Can you give us some more info on what's not working and what is the file format of the images you're uploading?

It may be that images are not ready to view until a tiled 'pyramid' has been generated. Do you see "clock" thumbnails? See this post for an example and discussion: viewtopic.php?f=4&t=7878

Thanks,

Will.

Indeed, there are clock-thumbnails visible. So the "pyramid" tip might be a good hint. I will give a feedback after a proof Thanks a lot!

Hi Michael

mkuhlmann wrote:Hello everybody,
Has it something to do with the used omero server? Thank you in advance for any help.

We did just have a problem with the pyramid generating service on the Demo
server, which has now been restarted.

Hopefully the pyramids will now be generated for your image(s).

This is highly unusual, and hopefully we will find the cause of the bug.

All the best,

Kenny

Yes, good hint - now it works - at least viewing the (pyramid) files. However, when I try to open them via the Fiji/ImageJ Plugin in Fiji I get the error message „An error occurred while loading the image“. Any idea?

If somebody wants to replicate my issue - the image ID is 182043. Thanks in advance.

Hi,

Large .jp2 files are known to cause difficulties, as the whole image must be decompressed (they cannot be read in tiles or sections). We have tried the test.jp2 file from QA 11365, and the large number of pixels suggests that you won't be able to open this in Fiji/ImageJ or successfully view in OMERO.

We're actively investigating such unique cases and we'll get back to you early next week, post a discussion within the team.

Best,
Balaji

Dear Balaji,
however, I did not use any .jp2-files for my Omero demo account. ID182043 is, like al our original images, a TIFF generated in Nikon NIS Elements. Any idea, Balaji? Anyway, thank you in advance

Best wishes,
Michael

Okay, now it works. I can open also the larger TIFFs without any problem. What did you alter, guys Anyway, when I now open them via the OMERO viewer everything is fine. But when I try to open them via Fiji/ImageJ (OMERO plugin) the RGB image is displayed as a three stack B/W image, in which each grayscale channel represents one color channel. I can correct this by clicking on >Color>Stack to RGB, but this generates a new file Does anybody know, how to open RGBs like RGBs? Thanks in advance!

Best wishes,
Michael

Sorry, nearly all files work, excepting the one with ID182043... Maybe, this last post was the result of Monday morning confusion