ImageJ Merging Channels

Question

I have written some codes below to process multichannel images, which invovle stacking, splitting and merging them back according to the order I have assigned.

// Run Z Project
run("Z Project...", "projection=[Sum Slices]");

// Split Channels
run("Split Channels");

// Get the number of open windows
nWindows = nImages();

// Create an array to store titles
windowTitles = newArray(nWindows);

// Loop through all open windows and store titles
for (i = 0; i < nWindows; i++) {
  // Select the i-th window
  selectImage(i + 1);  // ImageJ uses 1-based indexing

  // Get the title of the active window and store it in the array
  windowTitles[i] = getTitle();

  // Define identifiers
  identifier1 = "C1-";
  identifier2 = "C2-";
  identifier3 = "C3-";
  identifier4 = "C4-";
  identifier5 = "C5-";

  // Check if the title contains any of the identifiers
  if (
    windowTitles[i].indexOf(identifier1) != -1 ||
    windowTitles[i].indexOf(identifier2) != -1 ||
    windowTitles[i].indexOf(identifier3) != -1 ||
    windowTitles[i].indexOf(identifier4) != -1 ||
    windowTitles[i].indexOf(identifier5) != -1
  ) {
    // Run Merge Channels
    run("Merge Channels...", "c1=" + identifier5 + " c2=" + identifier2 + " c3=" + identifier1 + " c4=0 c5=0 c6=" + identifier5 + " c7=" + identifier3);
  }
}

However, error keeps showing up as it said: ')' expected in line 30 windowTitles[i].indexOf(identifier1) != -1 ||

Is there any ideas to fix this?

Thank you

Answer 1

From the code snippet, I don't see why you would get that error. However, the final merge command will not work because you are specifying first that "c1=C5-"... and you should not have a window with the name C5-. Also the "c4=0" will throw an error. Even if the merge command is fixed, the if statement doesn't make sense. One of the windows will always match so you would generate 5 merges that are all the same (because the arguments are variables that do not change).

A more simple approach: if you know that you will have 5 channels, you can just predict the names of the windows and write the merge that way.

title = getTitle();

// Run Z Project
run("Z Project...", "projection=[Sum Slices]");

// the title of this window is "SUM_" + original name
title = "SUM_" + title;

// Split Channels
run("Split Channels");

// do merge by predicting the names of the windows used
run("Merge Channels...", "c1=C5-" + title + " c2=C2-" + title + " c3=C1-" + title + " c6=C5-" + title + " c7=C3-" + title);

// add a save line here and then close everything
// close("*");

If you want to make the code more flexible then the approach you were trying is good, but it sounds like you have a specific task that needs automating and the snippet above should do the job.