[ome-users] CZI channel colour

Maier, Lorenz l.maier at dkfz-heidelberg.de
Sun May 11 10:51:08 BST 2014

Hi Roger,

could you reproduce the problem?
Or is there no problem and I am getting something wrong?


> Am 22.04.2014 um 12:53 schrieb "Maier, Lorenz" <l.maier at dkfz-heidelberg.de>:
> Dear Roger,
> even in composite mode, the image colors are changing with virtual stacks at my machine.
> I attached a minimal example macro, its input (czi) and my output (png).
> If I am not completely wrong, the "channel x.png" and "virtual channel x.png" should be exactly equal, but they are not.
> 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: Dienstag, 22. April 2014 11:53
> An: ome-users at lists.openmicroscopy.org.uk; Melissa Linkert
> Betreff: Re: [ome-users] CZI channel colour
> Hi Lorenz,
>> On 07/04/14 13:54, Maier, Lorenz wrote:
>> 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.
> If the mode is "Colourised" this is expected; if it's "Composite" you'll just see the border/text above changing colour (and the
> brightness+contrast dialogue histogram, if visible).
> This is a summary of the behaviour I see with both normal and virtual stacks (using the "hyperstack" viewer).  I don't see any difference if virtual stacks are on or off. (Gy=grey)
>             |         Stack type
> Colour mode | Full          Virtual
> ------------+--------------------------
> Default     | Gy -> RGBGy   Gy -> RGBGy
> Composite   | GBRGy         GBRGy
> Colourised  | GBRGy         GBRGy
> Greyscale   | Gy -> RGBGy   GY -> RGBGy
> Custom      | RGBGy         RGBGy
> Melissa, is there any way of making the plugin use the image-provided channel colours for Default and Greyscale, or is this information lost after the import when this is all passed to imagej from the importer?
> Would it also be possible to default the Custom channel colours to the image-provided colours?  It would be great if the behaviour was the same for all colour modes.
>> 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.
> This is useful to know, thanks!
> --
> 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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> <changing colors in composite mode.zip>

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