Macro for Auto Threshold to all Split Channels

[krura sandhu]

Hello,

I am very new to Image J and I'd be grateful for some help on making my macro capable to run auto threshold on the 3 split channels from any stained picture. The purpose is to split a multi channel image and run an auto threshold for each of the 3 split channels for any picture.  

So far the macro can convert the multi channel image to 8 bit and can perform the function "splitChannels"
However, the tittle of a stained picture prevents me to do auto threshold on a different stained picture.
I have defined the image tittle to be name = getTitle();
Additionally, I have associated the 3 split channels with these 3 variables.
C1 = "C1-"+name;
C2 = "C2-"+name;
C3 = "C3-"+name;

When I write "selectWindow C" prior to the auto threshold function, it prevent me to execute the line since there is "no window with the tittle C1 found." Should I define it as blue, green, or red?

Any suggestions will be great. I do not know if I have to create a new macro or continue with this macro.

run("8-bit");
run("Split Channels");
name = getTitle();
C1 = "C1-"+name;
C2 = "C2-"+name;
C3 = "C3-"+name;
run("Split Channels");
selectWindow("C1");
run("Auto Local Threshold", "method =Try all radius=100 parameter_1=0 parameter_2=0 white");
selectWindow("C2");
run("Auto Local Threshold", "method =Try all radius=100 parameter_1=0 parameter_2=0 white");
selectWindow("C3");
run("Auto Local Threshold", "method =Try all radius=100 parameter_1=0 parameter_2=0 white");



Thanks so much
Krura  

[Cammer, Michael]

You need to get the title before splitting the channels and not the syntax in the selectWindow command.  This works for me.

newImage("HyperStack", "16-bit composite-mode label", 400, 400, 3, 1, 1);
 run("8-bit");
 name = getTitle();
 run("Split Channels");
 C1 = "C1-"+name;
 C2 = "C2-"+name;
 C3 = "C3-"+name;
 selectWindow(C1);
 setAutoThreshold("Default dark");


_________________________________________
Michael Cammer, Optical Microscopy Specialist
http://ocs.med.nyu.edu/microscopy
http://microscopynotes.com/
Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of krura sandhu [[hidden email]]
Sent: Wednesday, July 26, 2017 12:58 PM
To: [hidden email]
Subject: Macro for Auto Threshold to all Split Channels

Hello,

I am very new to Image J and I'd be grateful for some help on making my
macro capable to run auto threshold on the 3 split channels from any stained
picture. The purpose is to split a multi channel image and run an auto
threshold for each of the 3 split channels for any picture.

So far the macro can convert the multi channel image to 8 bit and can
perform the function "splitChannels"
However, the tittle of a stained picture prevents me to do auto threshold on
a different stained picture.
I have defined the image tittle to be name = getTitle();
Additionally, I have associated the 3 split channels with these 3 variables.
C1 = "C1-"+name;
C2 = "C2-"+name;
C3 = "C3-"+name;

When I write "selectWindow C" prior to the auto threshold function, it
prevent me to execute the line since there is "no window with the tittle C1
found." Should I define it as blue, green, or red?

Any suggestions will be great. I do not know if I have to create a new macro
or continue with this macro.

run("8-bit");
run("Split Channels");
name = getTitle();
C1 = "C1-"+name;
C2 = "C2-"+name;
C3 = "C3-"+name;
run("Split Channels");
selectWindow("C1");
run("Auto Local Threshold", "method =Try all radius=100 parameter_1=0
parameter_2=0 white");
selectWindow("C2");
run("Auto Local Threshold", "method =Try all radius=100 parameter_1=0
parameter_2=0 white");
selectWindow("C3");
run("Auto Local Threshold", "method =Try all radius=100 parameter_1=0
parameter_2=0 white");



Thanks so much
Krura



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