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Cannot open large images

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Cannot open large images

Postby mkuhlmann » Fri Aug 21, 2015 9:34 am

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
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Re: Cannot open large images

Postby wmoore » Fri Aug 21, 2015 9:48 am

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.
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Re: Cannot open large images

Postby mkuhlmann » Fri Aug 21, 2015 10:13 am

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!
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Re: Cannot open large images

Postby kennethgillen » Fri Aug 21, 2015 10:40 am

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
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Re: Cannot open large images

Postby mkuhlmann » Fri Aug 21, 2015 10:48 am

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?
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Re: Cannot open large images

Postby mkuhlmann » Fri Aug 21, 2015 11:07 am

If somebody wants to replicate my issue - the image ID is 182043. Thanks in advance.
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Re: Cannot open large images

Postby bramalingam » Fri Aug 21, 2015 9:22 pm

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
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Re: Cannot open large images

Postby mkuhlmann » Mon Aug 24, 2015 8:29 am

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
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Re: Cannot open large images

Postby mkuhlmann » Mon Aug 24, 2015 9:17 am

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
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Re: Cannot open large images

Postby mkuhlmann » Mon Aug 24, 2015 9:46 am

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