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Nikon ics/ids ?

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Nikon ics/ids ?

Postby odbeki » Fri Nov 02, 2012 8:13 am

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

Postby jmoore » Fri Nov 02, 2012 9:46 am

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
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Re: Nikon ics/ids ?

Postby odbeki » Mon Nov 05, 2012 2:32 pm

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.
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Re: Nikon ics/ids ?

Postby jmoore » Mon Nov 05, 2012 9:51 pm

How large is the file? Could you provide it to us as a sample?
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Re: Nikon ics/ids ?

Postby odbeki » Tue Nov 06, 2012 7:06 am

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?
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Re: Nikon ics/ids ?

Postby mlinkert » Tue Nov 06, 2012 9:48 am

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.
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Re: Nikon ics/ids ?

Postby mlinkert » Fri Jan 04, 2013 9:04 pm

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.
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