Open Microscopy Environment

Using OMERO.insight for ImageJ, I tried to edit a large image (1.2 GB) in OMERO server, but the opening process failed with the error message "An error occurred while loading the image."

Opening another smaller image in the same dataset was successful.

Memory setting for ImageJ 24439 MB and should be big enough.


In the Console of ImageJ, the following messages were found.

Code: Select all

Parsing credentials
Logging in
Populating metadata
Parsing credentials
Logging in
Populating metadata
Parsing credentials
Logging in
Populating metadata

Any idea of what's wrong here?

Thanks in advance.

Cheers,
Kouichi

Hi,

I don't think the size should be a problem. Can you get a more informative output when you set the "Debug" option in ImageJ? If not, would it be possible to get the file ( https://www.openmicroscopy.org/qa2/qa/upload/ ), then I could try replicate/debug the problem.

Regards,
Dominik

Debug mode of ImageJ gave me exactly the same message as before.

I tried to download the image from OMERO.web, but it failed twice.

So I tried to upload the original from my local hard drive using your link. But although it says "1 file uploaded", I don't have any link or notification.

'Fused_imagej.tif' is the file name. Can you find it?

Hi Kouichi,

sorry, I didn't get the file (think there were some issues with the storage system yesterday). Could you please upload it again? I still can't replicate the issue with other example files unfortunately.

Cheers,
Dominik

It says '1 file uploaded.' again.

'Fused_imagej.tif' is the file name. Can you find it?

Dear Kouichi,

I am sorry for the hassle but can you try one more time? This week there were file storage issues here at Dundee that now appear to be resolved and our current QA file uploading app is poor at reporting errors. I just tried uploading a 1.2GB-ish file from outside Dundee and it arrived fine so with luck yours will too. If even a third try is unlucky then I'd see about getting somebody to get you credentials for uploading to us via FTP instead as we definitely want to investigate your issue. In the meantime we certainly appreciate your patience with these technical glitches.

Cheers,
Mark

I've done that again.

Any luck with the large image? I still can't do it.

By the way, I prepared that image by using Fiji's Stitching and saved as a standard TIFF.

I also tested one of the source tile images and opening it via OMERO.insight-ImageJ was successful. So, it may be related to Fiji's Stitching, if the size is not an issue.

I 've done further tests.

I've confirmed a single tile image (~32 MB) can be opened by OMERO.insight-ImageJ.

Instead of stitching the whole ~50 tiles, I stitched 6 tiles using FIji's Stitching. Saved them as TIFF or OME.TIFF (~140 MB each).

Contrary to my expectation, I was able to open both of them by OMERO.insight-ImageJ.

So it can possibly be a size issue.

My Fiji's memory allocation

Maximum memory: 24439 MB

Hi Kouichi,

thanks again for the upload. I imported the file on one of our testing servers and then tried to open it with the ImageJ Plugin. I had the same error. The detailed log showed that the Ice.MessageSizeMax was exceeded (that's a server setting, default is 250mb). It looks like the plugin tries to load a too big chunk of the data. Unfortunately I haven't found a workaround yet (e. g. if this property could be overwritten by a client setting, etc.).

Kind Regards,
Dominik