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I'm trying to write a code in Image J that will:

Open all images in separate windows that contains "488" within a folder Use look up tables to convert images to green and RGB color From ImageJ, the commands are: run("Green"); and run("RGB Color"); Adjust the brightness and contrast with defined values for Min and Max (same values for each image). I know that the code for that is:

//run("Brightness/Contrast..."); setMinAndMax(value min, value max); run("Apply LUT");

Save each image in the same, original folder , in Tiff and with the same name but finishing with "processed".

I have no experience with Java and am very bad with coding. I tried to piece something together using code I found on stackoverflow and on the ImageJ website, but kept getting error codes. Any help is much appreciated!

AgatheB
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1 Answers1

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I don't know if you still need it, but here is an example.

output_dir = "C:/Users/test/"
input_dir = "C:/Users/test/"

list = getFileList(input_dir);
listlength = list.length;

setBatchMode(true);
for (z = 0; z < listlength; z++){
    if(endsWith(list[z], 'tif')==true ){
        if(list[z].contains("488")){
        title = list[z];
            end = lengthOf(title)-4;
            out_path = output_dir + substring(title,0,end) + "_processed.tif";
            open(input_dir + title);
            //add all the functions you want
            run("Brightness/Contrast...");
            setMinAndMax(1, 15);
            run("Apply LUT");
            saveAs("tif", "" + out_path + "");
            close();
            };
    
        run("Close All");
        }
    }

setBatchMode(false);

I think it contains all the things you need. It opens all the images (in specific folder) that ends with tif and contains 488. I didn't completely understand what you want to do with each photo, so I just added your functions. But you probably won't have problems with adding more/different since you can get them with macro recorder. And the code is written to open tif files. If you have tiff just be cerful that you change that and also change -4 to -5.

Petra
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