How to make the plugin "Colocalisation Threshold" recordable in macro?

[Ales Kladnik]

Hello!
I'm trying to automate colocalization analysis with the "Colocalisation Threshold" plugin by Tony Collins, however, when I try to record a macro command for calling this plugin, I get "Duplicate keyword" errors regarding the keyword "channel".

this is the command that gets recorded:

run("Colocalisation Threshold", "channel=Eqt_celica1_R.tif channel=Eqt_celica1_G.tif use=[Channel 1] channel=[Red : Green] show");

I see there are multiple settings all labeled with "channel" - so my question is: is there a way to figure out the correct variable names, and pass them to the plugin from a macro?

-Ales Kladnik

[dscho]

Hi,

On Wed, 5 Aug 2009, Ales Kladnik wrote:

> I'm trying to automate colocalization analysis with the "Colocalisation
> Threshold" plugin by Tony Collins, however, when I try to record a macro
> command for calling this plugin, I get "Duplicate keyword" errors
> regarding the keyword "channel".

The easiest is to go back to the source and change the spaces to
underscores in the channel labels.

shameless plug: If you use Fiji, you can use Plugins>Compile and Run...
to compile and run the modified source, even if you did not install a Java
Development Kit.

Ciao,
Dscho

[Ales Kladnik]

Thanks, now it works great! I just didn't think of the possibility that passing variables to the plugin is done by names from the dialog - it's so simple I was looking past it. The underscored names in the source are now unique, and I can call the plugin from a macro.

Johannes Schindelin wrote

Hi,

On Wed, 5 Aug 2009, Ales Kladnik wrote:

> I'm trying to automate colocalization analysis with the "Colocalisation
> Threshold" plugin by Tony Collins, however, when I try to record a macro
> command for calling this plugin, I get "Duplicate keyword" errors
> regarding the keyword "channel".

The easiest is to go back to the source and change the spaces to
underscores in the channel labels.

shameless plug: If you use Fiji, you can use Plugins>Compile and Run...
to compile and run the modified source, even if you did not install a Java
Development Kit.

Ciao,
Dscho