I usually use the record function. Once all steps are recorded you can go through the macro text and each time the name of your image shows up you replace it with the word title. For example if the commend is selectWindow("C3-SomeImageName"); you would replace it with selectWindow("C3-"+title);

Subsequently copy this section in the beginning:

input = getDirectory("Choose an Input Directory");

output = getDirectory("Select a Results Directory")

function Macroname (input, output, filename) {

run("Bio-Formats", "open="+input+filename);

title=replace(filename,".zvi","");

If your files are not zvi, replace . zvi with whatever your format is. (If it's a .lif file containing multiple images you may need to change the command.) Then add your modified macro text with an indent aligning with the two lines above. At the end you probably want to add something like this

saveAs("PNG", output+title+".png");

run("Close");

Then close the function by adding:

}

and add this section at the end

setBatchMode(false);

list = getFileList(input);

for (i = 0; i < list.length; i++)

Macroname(input, output, list[i]);

Attached an example (I could not upload an ijm file)

There's a wait command to pause the macro for manual modifications. Here the documentation: https://imagejdocu.tudor.lu/plugin/utilities/wait_for_user/start

Hope that helps

Hi there,

The answer above is all right and is more of a BatchProcessing. You have also another option which is to assign a shortcut to your Macro so you just have to press a key to perform the function. In the example attached here is "F9". Btw, it will be much faster if you decide a value for each one of the channels for B&C adjustment so you can write it in the macro, this will prevent you for adjusting it in each channel each time. If you want to use different values for different sets of images, just rewrite the macro. The macro here automatically does all what you were doing, but image by image, by pressing F9. It will save the final image in the same folder where your original image was.

To use it:

Download the *.ijm file attached here.

Go to Plugins>Macro>Install...

Then open the image and press F9 and it will be done.

It also creates a white scale bar of 10*1 um at x=2um y=2um of your image. If you want to change those dimensions or the position, just modify the values 10 and 1 in the run("Specify..." line.

One warning, this is assuming that your C1=Red, C2=Green and C3=Blue. If it is not the case you have to modify the run("Merge Channels..." line. c1, c2 and c3 are always red, green, blue. If you have more channels, you will have to add them following the same reasoning.

Hope it helps,

Cheers

macro "adjust BC [F9]"

{

title = getTitle();

filename_clean = File.nameWithoutExtension();

path_to_dir = File.directory;

path_to_save = path_to_dir+filename_clean;

run("Z Project...", "projection=[Max Intensity]");

close(title);

run("Split Channels");

selectWindow("C1-MAX_"+title);

run("Brightness/Contrast...");

waitForUser("Apply optimal Brightness and contrast settings, then press OK");

selectWindow("C2-MAX_"+title);

run("Brightness/Contrast...");

waitForUser("Apply optimal Brightness and contrast settings, then press OK");

selectWindow("C3-MAX_"+title);

run("Brightness/Contrast...");

waitForUser("Apply optimal Brightness and contrast settings, then press OK");

run("Merge Channels...", "c1=C1-MAX_"+title+" c2=C2-MAX_"+title+" c3=C3-MAX_"+title+ "");

run("Specify...", "width=10 height=1 x=2 y=2 scaled");

setForegroundColor(255, 255, 255);

run("Fill");

saveAs("tiff", path_to_save+".tiff")

run("Close All");

}