We're Hiring!

"Open With" fails

General user discussion about using the OMERO platform to its fullest.
Please note:
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.

"Open With" fails

Postby Olaf » Thu Jan 05, 2017 3:56 pm

Dear all,

First of all a Happy 2017 for everybody!

I'm still a newby to OMERO and I am trying to use the "Open with" feature from OMERO.insight (5.2.6 - ice35).
Have a few nikon data sets (.nd2) importet. From the project I want to open the images via "open with" and then call NIS software. NIS software opens properly but the image is not open in NIS.
(Same happens when I use Fiji)

Running OMERO in a CentOS 7 on a VM (Hyper-V on a WIn Server 2012 R2)
The image data is actually sitting in a Folder / Repository on the Windows Filespace of the Win Serv 2012 machine that is mounted to the CentOS / OEMRO over a smb share.

Is there anyone who has an idea why the image data is not passed on from OMERO.insight to NIS or Fiji when I use "Open WIth"?

Thanks a lot!
Posts: 2
Joined: Wed Nov 30, 2016 3:05 pm

Re: "Open With" fails

Postby Dominik » Fri Jan 06, 2017 10:07 am

Hi Olaf,

I think the reason why "Open with" doesn't work with NIS viewer is, that it doesn't work with tif files. Because what happens when you use "Open with" is, that the image is exported as tif and passed on to the application you chose. If you want to use the proprietary software to open the image, you would have to download the original files from OMERO again. Buy you'd loose the connection to OMERO, ie. when annotating/changing the image you'd have to re-import the image again.

You can use "Open with" with Fiji, that should work. Do you get any error message when you tried to do that? However, I wouldn't recommend it. Because like said before, when using "Open with" you're working locally only, you'd loose the connection to OMERO. When you want to use Fiji or ImageJ I'd strongly suggest to use the OMERO Fiji/ImageJ plugin. This way you can work with the image in Fiji/ImageJ and synchronize your data (e.g. ROIs) back to OMERO.

User avatar
Team Member
Posts: 76
Joined: Mon Feb 10, 2014 11:26 am

Return to User Discussion

Who is online

Users browsing this forum: No registered users and 1 guest