[ome-users] CZI channel colour

[Roger Leigh]

I've tried with Fiji after updating it to the latest version, and this
is also working correctly I think, at least for me--I see green, blue,
red and white phase contrast.  The original metadata shows:

DisplaySetting|Channel|Color| #1        #FF00FF00
DisplaySetting|Channel|Color| #2        #FF0000FF
DisplaySetting|Channel|Color| #3        #FFFF0000

Which looks like green, blue, red in ABGR order.  Looking at the code
that parses this, we strip off the leading alpha and force it to FF in
all cases.  There isn't a colour for the fourth channel that I can see,
either in the original metadata or the OME-XML.  The above certainly
matches what I can see viewing the image.

It might be clearer if I could possibly see an image of what you're
seeing that's wrong.  If you think that might help, please feel free to
upload a screenshot to the QA system.


Regards,
Roger

On 04/04/2014 22:35, Roger Leigh wrote:
> 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
>>
>> The University of Dundee is a registered Scottish Charity, No:
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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
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


--
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