Nikon ics/ids ?
Posted:
Fri Nov 02, 2012 8:13 amby odbeki
Is it possible to use Omero for Nikon ics/ids files? I tried importing them, but they turn up in grayscale.
Re: Nikon ics/ids ?
Posted:
Fri Nov 02, 2012 9:46 amby jmoore
Hi Bertil,
OMERO/Bio-Formats do support ics/ids files: See
https://www.openmicroscopy.org/site/sup ... s/ics.htmlWould you be able to provide the file that you are having a problem with? Also, what version of OMERO are you using?
Cheers,
~Josh
Re: Nikon ics/ids ?
Posted:
Mon Nov 05, 2012 2:32 pmby odbeki
Hi,
Thanks for your reply. I just started trying out OMERO and downloaded "omero-vm-latest-build.ova" and OMERO clients 4.4.4 (
https://www.openmicroscopy.org/site/sup ... iance.html) and imported images with omero insight, but the images are in grayscale after import.
Re: Nikon ics/ids ?
Posted:
Mon Nov 05, 2012 9:51 pmby jmoore
How large is the file? Could you provide it to us as a sample?
Re: Nikon ics/ids ?
Posted:
Tue Nov 06, 2012 7:06 amby odbeki
It is 8.4 Mb. I tried to attach it but the upload function doesn\t work and he ics file was not accepted by the upload function. Could I e-mail it instead?
Re: Nikon ics/ids ?
Posted:
Tue Nov 06, 2012 9:48 amby mlinkert
You should be able to upload the file to OMERO.qa:
https://www.openmicroscopy.org/qa2/qa/upload/I will send alternate instructions in a private message in case that also does not work.
Re: Nikon ics/ids ?
Posted:
Fri Jan 04, 2013 9:04 pmby mlinkert
My apologies for not following up on this sooner.
There is now a fix for this problem under review:
https://github.com/openmicroscopy/bioformats/pull/328The next version of Bio-Formats/OMERO should import these .ics files correctly; in the meantime, setting the channel colors manually should give you an image that looks correct.