[ome-users] CZI channel colour

[Roger Leigh]

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