run("Merge Channels..." ...) problem

[BSdetector]

Could someone explain me why this works:

dir=getDirectory("Select a Directory");
image="no2_63x_32zoomb.lsm"
path=dir + image;
run("Bio-Formats", "open=path autoscale color_mode=Colorized view=Hyperstack stack_order=XYCZT stitch_tiles");
run("Magenta");
run("Split Channels");
selectWindow("C1-"+image);
Ch1 = getTitle;
selectWindow("C2-"+image);
Ch2 = getTitle;
selectWindow("C3-"+image);
Ch3 = getTitle;
run("Merge Channels...", "c2=C2-no2_63x_32zoomb.lsm c3=C3-no2_63x_32zoomb.lsm c6=C1-no2_63x_32zoomb.lsm create keep");

and this doesn't:
dir=getDirectory("Select a Directory");
image="no2_63x_32zoomb.lsm"
path=dir + image;
run("Bio-Formats", "open=path autoscale color_mode=Colorized view=Hyperstack stack_order=XYCZT stitch_tiles");
run("Magenta");
run("Split Channels");
selectWindow("C1-"+image);
Ch1 = getTitle;
selectWindow("C2-"+image);
Ch2 = getTitle;
selectWindow("C3-"+image);
Ch3 = getTitle;
run("Merge Channels...", "c2=Ch2 c3=Ch3 c6=Ch1 create keep");

???

Thanks,
B

[vbindokas]

You need to place a & before each variable in the quoted string.
Otherwise, it is looking for images named "Ch1", "Ch2", etc.

or, do

run("Merge Channels...", "c2="+Ch2+" c3="+Ch3+" c6="+Ch1+" create keep");


On 7/25/2016 7:39 AM, BSdetector wrote:

> Could someone explain me why this works:
>
> dir=getDirectory("Select a Directory");
> image="no2_63x_32zoomb.lsm"
> path=dir + image;
> run("Bio-Formats", "open=path autoscale color_mode=Colorized view=Hyperstack
> stack_order=XYCZT stitch_tiles");
> run("Magenta");
> run("Split Channels");
> selectWindow("C1-"+image);
> Ch1 = getTitle;
> selectWindow("C2-"+image);
> Ch2 = getTitle;
> selectWindow("C3-"+image);
> Ch3 = getTitle;
> run("Merge Channels...", "c2=C2-no2_63x_32zoomb.lsm
> c3=C3-no2_63x_32zoomb.lsm c6=C1-no2_63x_32zoomb.lsm create keep");
>
> and this doesn't:
> dir=getDirectory("Select a Directory");
> image="no2_63x_32zoomb.lsm"
> path=dir + image;
> run("Bio-Formats", "open=path autoscale color_mode=Colorized view=Hyperstack
> stack_order=XYCZT stitch_tiles");
> run("Magenta");
> run("Split Channels");
> selectWindow("C1-"+image);
> Ch1 = getTitle;
> selectWindow("C2-"+image);
> Ch2 = getTitle;
> selectWindow("C3-"+image);
> Ch3 = getTitle;
> run("Merge Channels...", "c2=Ch2 c3=Ch3 c6=Ch1 create keep");
>
> ???
>
> Thanks,
> B
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/run-Merge-Channels-problem-tp5016934.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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Vytas Bindokas, Ph.D.
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Director, BSD Light Microscopy Core Facility
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