Stackreg colour problem

[Paul Wieringa]

Dear all,

I'm a recent ImageJ convert using ImageJ to manipulate *.lsm stack files
(the Carl Zeiss LSM file format). My images are of FITC-labelled neurons.

I'm currently trying to use stackReg, which appears to work beautifully for
alignment. However, it does not return my stack to the original colour.
I've read on the stackreg website that the conversion to a grayscale image
is expected (necessary for alignment?) but that the colour is then supposed
to be changed back to the original. In my case, this last step is evidently
not happening.

Has anyone experienced anything similar? Any suggestions? I've looked at the
code, but would really prefer to not have to try and hack this plugin - it's
a bit intimidating.

Any help greatly appreciated!

Regards,
Paul Wieringa

[jmutterer]

Paul, StackReg can be called from a macro. You can use a simple macro that
remembers the current LUT, runs StackReg, and restores the LUT :

macro "StackReg with LUT [F1]"{
getLut(r,g,b);
run("StackReg ", "transformation=[Rigid Body]");
setLut(r,g,b);}

Jerome

On Jan 22, 2008 1:05 PM, Paul Wieringa <[hidden email]> wrote:

> Dear all,
>
> I'm a recent ImageJ convert using ImageJ to manipulate *.lsm stack files
> (the Carl Zeiss LSM file format). My images are of FITC-labelled neurons.
>
> I'm currently trying to use stackReg, which appears to work beautifully
> for
> alignment. However, it does not return my stack to the original colour.
> I've read on the stackreg website that the conversion to a grayscale image
> is expected (necessary for alignment?) but that the colour is then
> supposed
> to be changed back to the original. In my case, this last step is
> evidently
> not happening.
>
> Has anyone experienced anything similar? Any suggestions? I've looked at
> the
> code, but would really prefer to not have to try and hack this plugin -
> it's
> a bit intimidating.
>
> Any help greatly appreciated!
>
> Regards,
> Paul Wieringa
>