[ome-users] CZI channel colour

[Maier, Lorenz]

Hi Roger,

thanks for looking into this problem!
I just downloaded a fresh copy of the continuous release version of Fiji and I still have that problem.

It seems to be correlated to the color info being denoted with or without alpha channel (in the "Info" window of Fiji showing the meta-information).
With an alpha-channel (e.g. #FFFF0000 instead of #FF0000 for red), the channels are all displayed in white.

I would assume it will be fixed with the 5.0.1 release, as the color-information format for CZI specified on the "supported formats" page already shows an alpha channel.

Best regards,
Lorenz

-----Ursprüngliche Nachricht-----
Von: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] Im Auftrag von Roger Leigh
Gesendet: Freitag, 4. April 2014 20:17
An: Maier, Lorenz; ome-users at lists.openmicroscopy.org.uk
Betreff: Re: [ome-users] Imaris .ims wrong number of channels

On 01/04/2014 13:12, Maier, Lorenz wrote:
> Dear all,
>
> there seems to be an error in the number of channels detected for 
> Imaris files (.ims 5.5 format, generated with Imaris 7.7).
>
> Fiji opens shows only one of the channels. I've uploaded an example on
> https://www.openmicroscopy.org/qa2/qa/feedback/8019 .

Hi,

In case you didn't get the reply from the QA system for #8022 (CZI channel colour), following up here as well.

I've checked this CZI image with the current 5.0.x build of the loci_tools plugin and ImageJ 1.48s.  It's displaying green/blue/red/white correctly as far as I can tell. I imported your image into ImageJ using the Bio-Formats importer with either "Composite"
or "Colourised" channel mode selected and the channels all appear as the correct colour. (The channel mode shouldn't affect the import itself though, just the default view mode.)

Which version of the Bio-Formats plugin were you using?

Depending upon which version of the plugin you are using, it's possible that this might be fixed in the upcoming 5.0.1 release next week, but if you're using a 4.4 version of the plugin, it would be worth checking with 5.0.0.

Regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________
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