[ome-users] CZI channel colour

[Roger Leigh]

Hi Lorenz,

Thanks for the feedback, I'll double-check with Fiji and see if it's an
issue with the plugin or with the specific Fiji/ImageJ it's being used
with.  In the meantime, it might be worth giving plain ImageJ a try to
see if that works?  (This is what I was testing with.)


Regards,
Roger

On 04/04/2014 21:17, Maier, Lorenz wrote:
> 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
>
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--
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