Zeis .zvi channel specification

[Hoeppner, Daniel (NIH/NINDS) [E]]

Hello List,

I wish to apply a macro to only a single channel of a multi-channel Zeiss .zvi file.  Thank you in advance for advice on how to specify channels.

Dan

[dscho]

Hi Dan,

On Tue, 9 Nov 2010, Hoeppner, Daniel (NIH/NINDS) [E] wrote:

> I wish to apply a macro to only a single channel of a multi-channel
> Zeiss .zvi file.  Thank you in advance for advice on how to specify
> channels.

The easiest is probably to choose the channel and then run Reduce
Dimensionality... unchecking the channels, keeping the original image. In
effect you'd duplicate just that channel. In macro code:

        // make the second channel the active one
        Stack.setChannel(2);
        // duplicate just that channel
        run("Reduce Dimensionality...", "slices keep");

Just paste your macro after that, or run it with something like
runMacro("/Users/hoeppner/my-macros/magic.ijm");

Ciao,
Johannes