Need help with a macro for changing channels and colors in the "run("Arrange Channels...");" function.

[MrScientistman2]

Hi all,

Im trying to set up a macro that automatically assigns either of the RGB colors (according to my specific needs) to the various channels in a confocal-stack (with 3 channels). I can do this perfectly well manually with the Image->Color->Arrange Channels tool, but would like to program it to a macro. Ive tried to manipulate the "run("Arrange Channels...");" command but I dont know if it can do what im looking for.

What I want: Assign red to channel 1, green to channel 2, and blue to channel 3, and at a later point leave red at channel 1, move the blue channel to channel 2 and make it green, and move the green (old channel 2) to channel 3 and make it blue. Are there any options embedded in this function that would do such a thing? Or are there any other solutions?

I hope anyone can help me!

[Kenton Arkill]

Can't check here about arrange channels, but I normally use merge and split
for similar work. The names aways end in different letters after the split
(so if(endswith()) is useful).
Regards
Kenton


On 24 May 2014 22:35, MrScientistman2 <[hidden email]> wrote:

> Hi all,
>
> Im trying to set up a macro that automatically assigns either of the RGB
> colors (according to my specific needs) to the various channels in a
> confocal-stack (with 3 channels). I can do this perfectly well manually
> with
> the Image->Color->Arrange Channels tool, but would like to program it to a
> macro. Ive tried to manipulate the "run("Arrange Channels...");" command
> but
> I dont know if it can do what im looking for.
>
> What I want: Assign red to channel 1, green to channel 2, and blue to
> channel 3, and at a later point leave red at channel 1, move the blue
> channel to channel 2 and make it green, and move the green (old channel 2)
> to channel 3 and make it blue. Are there any options embedded in this
> function that would do such a thing? Or are there any other solutions?
>
> I hope anyone can help me!
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Need-help-with-a-macro-for-changing-channels-and-colors-in-the-run-Arrange-Channels-function-tp5007906.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[bnorthan]

Hi Mr. Scientist

Do you have a reason to actually move the blue to channel 2??  If so using
the merge and split like Kenton suggested is probably a good idea.

I've been working with some images where I just need to assign a new color
to each channel.  A simple Macro like this seems to work - Brian

Stack.setChannel(1)
run("Blue");

Stack.setChannel(2)
run("Red");

Stack.setChannel(3)
run("Green");


On Sun, May 25, 2014 at 7:54 AM, Kenton Arkill <[hidden email]>wrote:

> Can't check here about arrange channels, but I normally use merge and split
> for similar work. The names aways end in different letters after the split
> (so if(endswith()) is useful).
> Regards
> Kenton
>
>
> On 24 May 2014 22:35, MrScientistman2 <[hidden email]> wrote:
>
> > Hi all,
> >
> > Im trying to set up a macro that automatically assigns either of the RGB
> > colors (according to my specific needs) to the various channels in a
> > confocal-stack (with 3 channels). I can do this perfectly well manually
> > with
> > the Image->Color->Arrange Channels tool, but would like to program it to
> a
> > macro. Ive tried to manipulate the "run("Arrange Channels...");" command
> > but
> > I dont know if it can do what im looking for.
> >
> > What I want: Assign red to channel 1, green to channel 2, and blue to
> > channel 3, and at a later point leave red at channel 1, move the blue
> > channel to channel 2 and make it green, and move the green (old channel
> 2)
> > to channel 3 and make it blue. Are there any options embedded in this
> > function that would do such a thing? Or are there any other solutions?
> >
> > I hope anyone can help me!
> >
> >
> >
> > --
> > View this message in context:
> >
> http://imagej.1557.x6.nabble.com/Need-help-with-a-macro-for-changing-channels-and-colors-in-the-run-Arrange-Channels-function-tp5007906.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[MrScientistman2]

Thanks a bunch guys! This is exactly what I needed. Also, it turned out I didnt need to rearrange the channels (it was for the RG2B plugin).