[ome-users] CZI channel colour

Mon Apr 7 13:54:54 BST 2014

Dear Roger,

if I select "virtual stacks" in an czi image of the same type as on QA and I change the displayed channel, not only the border color changes, but the whole image.

You are right about the display settings of LSM files: if a channel is blue, but set not to be displayed, its LUT in ImageJ is all black. For CZIs, that's not  the case. And personally, I like the CZI behavior better. (Just for clearing up things, no wish for a change.)

The LUT with value 127 at position 0 occur to me inside ImageJ for a different set of CZI images. Those were saved with Zen black 2012 SP1, instead of Zen blue 2012 SP2. Even re-saving them with Zen blue without any further changes removes the effect.

Best,
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: Montag, 7. April 2014 14:00
An: ome-users at lists.openmicroscopy.org.uk
Betreff: Re: [ome-users] CZI channel colour

Hi Lorenz,

It certainly looks odd that the "Default" and "Greyscale" options don't behave the same way as Composite/Colour.  That doesn't seem quite right.
  I'll check if this is by design or if it's a bug in the plugin or in ImageJ, and open a ticket if this is the case.  I would have thought that the channel colour in the original image should be correctly retained in each case.

The border colour in the composite image is usually the colour of the channel as it would appear in "Color" mode (though of course in "Composite" mode you are seeing all channels, so switching channels makes no obvious difference.

The channel display setup during acquisition does affect the metadata in the image file.  At least, this was certainly the case when saving LSM files from Zen; it's likely to be the same for CZI as well.  There is certainly colour data for the first three channels, and none for the fourth channel.

Regarding the LUT, is this one saved with the original image, or one you applied in imagej?

Kind regards,
Roger

On 05/04/2014 14:37, Maier, Lorenz wrote:
> Hi Roger,
>
> so far I always used "Default" color mode when importing and applied "Make Composite" afterwards.
> This worked correctly, but only for czi images that store the colors without alpha channel in the meta information.
> Converting images with alpha channel to composite after importing defaults to r,g,b,white channel colors.
>
> As you pointed out, directly importing with the "colorized" or "composite" option correctly applies the colors in any case - thanks!
>
> A few last questions: what's the logic behind the change of colors when I select different channels in the composite image? Somehow I remember only a changing border color, but now the whole image changes.
>
> Why does the LUT sometimes contain 127 at position 0?
>
> And could it be that channels that were set not to be displayed in Zen (the Zeiss software creating the .czis) are treated differently? I think they were white, when I imported them probably with Default color mode.
>
>
> Thanks a lot,
> 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: Samstag, 5. April 2014 01:59
> An: ome-users at lists.openmicroscopy.org.uk
> Betreff: Re: [ome-users] CZI channel colour
>
> 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:
>>> SC015096 _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>> _______________________________________________
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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 _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> _______________________________________________
> 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 _______________________________________________
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