Nikon ics/ids ?

[odbeki]

Is it possible to use Omero for Nikon ics/ids files? I tried importing them, but they turn up in grayscale.

[jmoore]

Hi Bertil,


OMERO/Bio-Formats do support ics/ids files: See https://www.openmicroscopy.org/site/sup ... s/ics.html

Would you be able to provide the file that you are having a problem with? Also, what version of OMERO are you using?

Cheers,
~Josh

[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.

[jmoore]

How large is the file? Could you provide it to us as a sample?

[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?

[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.

[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/328

The 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.