ImageJ

Merge 4 color channels

_‹ Previous Topic Next Topic _›

Classic

List

Threaded

6 messages Options

woojkim

Merge 4 color channels

I'm trying to 4 color image ND2 files into separate color, adjust each color with different parameters, and re-merge them into a single file in a batch mode. The script I wrote is below. At the end of macro, it stops with a dialog box saying " Merge Channels There must be at least one source image or stack [OK]". Could anyone help me to fix it?

dir1 = getDirectory('Choose Directory ');
list = getFileList(dir1);
dir2 = dir1+"JPG"+File.separator;
File.makeDirectory(dir2);

setBatchMode(true);
for (i=0; i<list.length; i++) {
print(dir1 + list[i]);
showProgress(i, list.length);
name = dir1 + list[i];

run("Bio-Formats Importer", "open=name view=Hyperstack stack_order=XYCZT Color mode=Default split_channels");
name1 = list[i];
index = lastIndexOf(name1, ".");
if (index!=-1) name2 = substring(name1, 0, index);
path = dir2 + name2;
print(path);

selectWindow(name1 + ' - C=0');
run("Channels Tool...");
run("Green");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 50);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=1');
run("Channels Tool...");
run("Blue");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 150);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=2');
run("Channels Tool...");
run("Yellow");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 35);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=3');
run("Channels Tool...");
run("Magenta");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 100);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");
selectWindow("Channels");
run("Close");

selectWindow(name1 + ' - C=0');
green = getTitle;
selectWindow(name1 + ' - C=1');
blue = getTitle;
selectWindow(name1 + ' - C=2');
yellow = getTitle;
selectWindow(name1 + ' - C=3');
magenta = getTitle;

print(green);
print(blue);
print(yellow);
print(magenta);

run("Merge Channels...",
"C2=green C3=blue C6=yellow C7=magenta keep");
saveAs("jpeg", path + ".jpg");
run("Close");
}

Straub, Volko A. (Dr.)

Re: Merge 4 color channels

Try changing the last line of your macro to:

run("Merge Channels...",
"C2="+green+" C3="+blue+" C6="+yellow+" C7="+magenta+" keep");
saveAs("jpeg", path + ".jpg");
run("Close");
}

green, blue, yellow and magenta are variable names that hold the titles of your images. In your version of the code, the code looks for images called 'green', 'blue', etc.

Hope this helps,
Volko

On 21/05/2015 20:42, woojkim wrote:

> I'm trying to 4 color image ND2 files into separate color, adjust each color
> with different parameters, and re-merge them into a single file in a batch
> mode. The script I wrote is below. At the end of macro, it stops with a
> dialog box saying " Merge Channels There must be at least one source image
> or stack [OK]". Could anyone help me to fix it?
>
>
> dir1 = getDirectory('Choose Directory ');
> list = getFileList(dir1);
> dir2 = dir1+"JPG"+File.separator;
> File.makeDirectory(dir2);
>
> setBatchMode(true);
> for (i=0; i<list.length; i++) {
> print(dir1 + list[i]);
> showProgress(i, list.length);
> name = dir1 + list[i];
>
> run("Bio-Formats Importer", "open=name view=Hyperstack stack_order=XYCZT
> Color mode=Default split_channels");
> name1 = list[i];
> index = lastIndexOf(name1, ".");
> if (index!=-1) name2 = substring(name1, 0, index);
> path = dir2 + name2;
> print(path);
>
> selectWindow(name1 + ' - C=0');
> run("Channels Tool...");
> run("Green");
> run("RGB Color");
> run("Brightness/Contrast...");
> setMinAndMax(8, 50);
> call("ij.ImagePlus.setDefault16bitRange", 8);
> selectWindow("B&C");
> run("Close");
>
> selectWindow(name1 + ' - C=1');
> run("Channels Tool...");
> run("Blue");
> run("RGB Color");
> run("Brightness/Contrast...");
> setMinAndMax(8, 150);
> call("ij.ImagePlus.setDefault16bitRange", 8);
> selectWindow("B&C");
> run("Close");
>
> selectWindow(name1 + ' - C=2');
> run("Channels Tool...");
> run("Yellow");
> run("RGB Color");
> run("Brightness/Contrast...");
> setMinAndMax(8, 35);
> call("ij.ImagePlus.setDefault16bitRange", 8);
> selectWindow("B&C");
> run("Close");
>
> selectWindow(name1 + ' - C=3');
> run("Channels Tool...");
> run("Magenta");
> run("RGB Color");
> run("Brightness/Contrast...");
> setMinAndMax(8, 100);
> call("ij.ImagePlus.setDefault16bitRange", 8);
> selectWindow("B&C");
> run("Close");
> selectWindow("Channels");
> run("Close");
>
> selectWindow(name1 + ' - C=0');
> green = getTitle;
> selectWindow(name1 + ' - C=1');
> blue = getTitle;
> selectWindow(name1 + ' - C=2');
> yellow = getTitle;
> selectWindow(name1 + ' - C=3');
> magenta = getTitle;
>
> print(green);
> print(blue);
> print(yellow);
> print(magenta);
>
> run("Merge Channels...",
> "C2=green C3=blue C6=yellow C7=magenta keep");
> saveAs("jpeg", path + ".jpg");
> run("Close");
> }
>
>
>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Merge-4-color-channels-tp5012905.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

woojkim

Re: Merge 4 color channels

Dear Volko Straub,

I tried as you suggested, but it shows the same dialog box...
Any other suggestion?
Thank you very much!

Woo Jae

Straub, Volko A. (Dr.)

Re: Merge 4 color channels

Okay, I had a closer look at your code. There were another few problems.
First, when you use the Bio-Formats Importer the first time, you also
need to combine the name variable with the rest of the string as I
mentioned in my last email. I would also suggest that you put square
brackets before and after the name variable to make sure that spaces in
your file names are included.
Second, all the commands are case sensitive. So, when you use color_mode
to pass an arguement to the Bio-Formats Importer, you need to use
color_mode, not Color_mode. The same applies to c2, c3 (not C2, C3) in
the merge command.
I modified the code below and it appears to be working. If you copy it,
just be aware of any line breaks that might have been introduced by the
email programme.
Finally, the code seems rather complicated for what you want to achieve.
If you simply want to assign specific colours to individual channels and
adjust their brightness, why don't you just open the image with the
Bio-Formats Importer without using the 'Split channel' option, but
select 'Composite' as Color Mode? You could then use the 'Channels Tool
- More' to assign specific colors to each channel. You should also be
able to individually adjust the brightness/contrast for each channel.
Hope this solves your issues,
Volko

Modified macro code:

dir1 = getDirectory('Choose Directory ');
list = getFileList(dir1);
dir2 = dir1+"JPG"+File.separator;
File.makeDirectory(dir2);

setBatchMode(true);
for (i=0; i<list.length; i++) {
print(dir1 + list[i]);
showProgress(i, list.length);
name = dir1 + list[i];

run("Bio-Formats Importer", "open=["+name+"] view=Hyperstack
stack_order=XYCZT color_mode=Default split_channels"); //name is
variable; put [ ] around string variable to include potential spaces in
filename; color_mode, not Colour mode
name1 = list[i];
index = lastIndexOf(name1, ".");
if (index!=-1) name2 = substring(name1, 0, index);
path = dir2 + name2;
print(path);

selectWindow(name1 + ' - C=0');
run("Channels Tool...");
run("Green");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 50);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=1');
run("Channels Tool...");
run("Blue");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 150);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=2');
run("Channels Tool...");
run("Yellow");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 35);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=3');
run("Channels Tool...");
run("Magenta");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 100);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");
selectWindow("Channels");
run("Close");

selectWindow(name1 + ' - C=0');
green = getTitle;
selectWindow(name1 + ' - C=1');
blue = getTitle;
selectWindow(name1 + ' - C=2');
yellow = getTitle;
selectWindow(name1 + ' - C=3');
magenta = getTitle;

print(green);
print(blue);
print(yellow);
print(magenta);

run("Merge Channels...", "c2=["+green+"] c3=["+blue+"] c6=["+yellow+"]
c7=["+magenta+"] keep"); // c2, not C2 (small c, commands are case
sensitive); use [] around string variables to include spaces in filenames
saveAs("jpeg", path + ".jpg");
run("Close");
}

On 22/05/2015 15:25, woojkim wrote:

> Dear Volko Straub,
>
> I tried as you suggested, but it shows the same dialog box...
> Any other suggestion?
> Thank you very much!
>
> Woo Jae
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Merge-4-color-channels-tp5012905p5012915.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

Cammer, Michael

Re: Merge 4 color channels

Do either of these help?

http://microscopynotes.com/imagej/macros/color_channels_macro_v100.txt
http://microscopynotes.com/imagej/macros/composite-colors/user-selected-contrast-colors-names-save8bit.html

_________________________________________
Michael Cammer, Optical Microscopy Specialist
http://ocs.med.nyu.edu/microscopy
http://microscopynotes.com/
Cell: (914) 309-3270

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Volko Straub [[hidden email]]
Sent: Saturday, May 23, 2015 2:09 AM
To: [hidden email]
Subject: Re: Merge 4 color channels

Okay, I had a closer look at your code. There were another few problems.
First, when you use the Bio-Formats Importer the first time, you also
need to combine the name variable with the rest of the string as I
mentioned in my last email. I would also suggest that you put square
brackets before and after the name variable to make sure that spaces in
your file names are included.
Second, all the commands are case sensitive. So, when you use color_mode
to pass an arguement to the Bio-Formats Importer, you need to use
color_mode, not Color_mode. The same applies to c2, c3 (not C2, C3) in
the merge command.
I modified the code below and it appears to be working. If you copy it,
just be aware of any line breaks that might have been introduced by the
email programme.
Finally, the code seems rather complicated for what you want to achieve.
If you simply want to assign specific colours to individual channels and
adjust their brightness, why don't you just open the image with the
Bio-Formats Importer without using the 'Split channel' option, but
select 'Composite' as Color Mode? You could then use the 'Channels Tool
- More' to assign specific colors to each channel. You should also be
able to individually adjust the brightness/contrast for each channel.
Hope this solves your issues,
Volko

Modified macro code:

dir1 = getDirectory('Choose Directory ');
list = getFileList(dir1);
dir2 = dir1+"JPG"+File.separator;
File.makeDirectory(dir2);

setBatchMode(true);
for (i=0; i<list.length; i++) {
print(dir1 + list[i]);
showProgress(i, list.length);
name = dir1 + list[i];

run("Bio-Formats Importer", "open=["+name+"] view=Hyperstack
stack_order=XYCZT color_mode=Default split_channels"); //name is
variable; put [ ] around string variable to include potential spaces in
filename; color_mode, not Colour mode
name1 = list[i];
index = lastIndexOf(name1, ".");
if (index!=-1) name2 = substring(name1, 0, index);
path = dir2 + name2;
print(path);

selectWindow(name1 + ' - C=0');
run("Channels Tool...");
run("Green");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 50);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=1');
run("Channels Tool...");
run("Blue");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 150);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=2');
run("Channels Tool...");
run("Yellow");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 35);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=3');
run("Channels Tool...");
run("Magenta");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 100);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");
selectWindow("Channels");
run("Close");

selectWindow(name1 + ' - C=0');
green = getTitle;
selectWindow(name1 + ' - C=1');
blue = getTitle;
selectWindow(name1 + ' - C=2');
yellow = getTitle;
selectWindow(name1 + ' - C=3');
magenta = getTitle;

print(green);
print(blue);
print(yellow);
print(magenta);

run("Merge Channels...", "c2=["+green+"] c3=["+blue+"] c6=["+yellow+"]
c7=["+magenta+"] keep"); // c2, not C2 (small c, commands are case
sensitive); use [] around string variables to include spaces in filenames
saveAs("jpeg", path + ".jpg");
run("Close");
}

On 22/05/2015 15:25, woojkim wrote:

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

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

woojkim

RE: Merge 4 color channels

In reply to this post by Straub, Volko A. (Dr.)

Dear Volko,

It works! Great! Thank you very much!

Woo Jae

From: Volko Straub [via ImageJ] [mailto:ml-node+[hidden email]]
Sent: Saturday, May 23, 2015 2:07 AM
To: Kim, Woo Jae
Subject: Re: Merge 4 color channels

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

If you reply to this email, your message will be added to the discussion below:

http://imagej.1557.x6.nabble.com/Merge-4-color-channels-tp5012905p5012923.html

To unsubscribe from Merge 4 color channels, click here.
NAML

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.