[ome-users] CZI channel colour
rleigh at dundee.ac.uk
Mon May 12 14:52:12 BST 2014
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.
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?
>> 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.
>> -----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 _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> <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
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