We're Hiring!

Cannot open large images

General user discussion about using the OMERO platform to its fullest. Please ask new questions at https://forum.image.sc/tags/omero
Please note:
Historical discussions about OMERO. Please look for and ask new questions at https://forum.image.sc/tags/omero

There are workflow guides for various OMERO functions on our help site - http://help.openmicroscopy.org

You should find answers to any basic questions about using the clients there.

Re: Cannot open large images

Postby bramalingam » Wed Aug 26, 2015 2:22 pm

Hi,

Regarding the opening of RGB images on ImageJ:
The “Color mode" needs to be set to “Composite” in the “Bio-Formats Import options” window, while opening the image.
Please let us know if this does not solve your issue.

Regarding the image: ID182043
Although there was a performance issue, we were still able to generate the pyramids on our test-server.
And I was able to view the image with both the clients (web and insight).

The performance issue can be attributed to the way, Bio-Formats scans and reads the tiles from the file.
I have created a ticket on this regard,
https://trac.openmicroscopy.org/ome/ticket/13004
and have added you to the cc list.

Notifications will be sent to your email id, when there is a status change on the ticket.

Best,
Balaji
User avatar
bramalingam
 
Posts: 70
Joined: Tue Jan 14, 2014 12:01 pm

Re: Cannot open large images

Postby mkuhlmann » Thu Aug 27, 2015 10:48 am

Dear Balaji,
thanks for the hints. To open the RGB pictures via bioformats works now.

However, no change regarding ID182043. I agree, to directly open the image in OMERO.web or OMERO.insight is not a problem at all. The issue is to open it in ImageJ/Fiji via the respective OMERO plugin. This is quite important for me, because the OMERO image viewer does not allow image editing.

Best regards,
Michael
mkuhlmann
 
Posts: 8
Joined: Thu Aug 20, 2015 2:45 pm

Re: Cannot open large images

Postby bramalingam » Fri Aug 28, 2015 1:54 pm

Hi,

Due to memory management issues, opening the whole image in ImageJ using the Omero-IJ plugin is not possible, currently.

I have filed a ticket on this regard,
https://trac.openmicroscopy.org/ome/ticket/13014
and you have been added to the cc list.

Could you give us more information on your "image editing" workflow. I can check if we can suggest some round-about options (for the time-being) to suit your workflow.

ex: We can create images from ROI's using scripts in OMERO and those images can be opened in ImageJ (individually).Post processing the individual images can be stitched together and be sent back to OMERO.

Best,
Balaji
User avatar
bramalingam
 
Posts: 70
Joined: Tue Jan 14, 2014 12:01 pm

Previous

Return to User Discussion

Who is online

Users browsing this forum: No registered users and 1 guest