[ome-users] CZI channel colour

[Roger Leigh]

Hi Lorenz,

Using the macro you provided in your previous email, I can indeed see
the problem.  Something odd is definitely happening using virtual
stacks.  But, if I take the virtual stack and switch from composite to
colour and back again it all works the same as if it was a non-virtual
stack.  Something seems to not be set up quite right when loading a
virtual stack from a macro, but I'm not sure what that is.  I'll open a
ticket for this and investigate this further.


Regards,
Roger


On 11/05/14 10:51, Maier, Lorenz wrote:
> Hi Roger,
>
> could you reproduce the problem?
> Or is there no problem and I am getting something wrong?
>
> Best,
> Lorenz
>
>> 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
>>
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>> <changing colors in composite mode.zip>
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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