Use ImageJ macro to facilitate and automate image processing

Well, first of first, read the following introduction carefully
http://rsbweb.nih.gov/ij/developer/macro/macros.html (google cache)

There is a workshop going on right now. I sit through half of it and realized that all I need to know is what functions she used (Macros.zip). Because, I use ImageJ macro a lot (one example).

Here are my notes from her code.

• ImageJ 2 is coming, combined effect of BioFormat, Fiji, ImageJ
• in macro window, highlight the rows then command+r / ctrl+r will only execute part of the code, perfect for debugging
• start from recording your own macro (menu: macro - record), and understand its code
• nSlices for the slice number of an image stack (z stack or time lapse)

• exist1 = File.isDirectory(pathToSaveTo + "max");
  if (exist1 != 1) {
  	File.makeDirectory(pathToSaveTo + "max");
  }

• for (i = 1; i <= n; i ++) { // looping code}

• for (n = 1; n <= nSlices; n ++){
  	setSlice(n); // go to slice n
  	run("Measure");
  }

• for (n = 1; n <= nSlices; n ++) {
  	setSlice(n);
  	getStatistics(area, mean, min, max, stdev);
  	if (mean > maxMean) {
  		maxMean = mean;	//if it is larger than maxMean, then mark this slice as the new maxMean
  		frameToDup = n;
  	}
  }

• orig = getImageID;
  
  newImage("cropped", "16-bit Black", 300, 300, nSlices);
  final = getImageID;
  
  setBatchMode(true);
  for (n = 1; n <= nSlices; n ++) {
  	selectImage(orig);
  	setSlice(n);
  	run("Copy");
  	selectImage(final);
  	setSlice(n);
  	run("Paste");
  }
  setBatchMode(false);
  
  //find the frame with the maximum intensity, go to that frame and reset brightness/contrast
  maxmax =0;
  setBatchMode(true);
  for (n = 1; n <= nSlices; n ++) {
  	setSlice(n);
  	getStatistics(area, mean, min, max);
  	if (max > maxmax) {
  		maxmax = max;
  		nofmax = n;
  	}
  }
  setBatchMode(false);
  
  // now go to slice with the maxmax and use that to reset intensities in the stack
  setSlice(nofmax);
  run("Brightness/Contrast...");
  resetMinAndMax();
  
  //convert the new stack into 8-bit, which is required for 3D volume projection
  selectImage(final);
  run("8-bit");
  //run the 3D projection viewer. Do a "record macro" to get your settings right. Make sure to enter the appropriate xy to z pixel ratio
  //for example, 200nm steps with 61nm/pixel in x,y is a ratio of 3.28
  run("3D Project...", "projection=[Brightest Point] axis=Y-Axis slice=3.28 initial=0 total=360 rotation=9 lower=1 upper=255 opacity=0 surface=100 interior=50 interpolate");

• resetMinAndMax(), With 16-bit and 32-bit images, resets the minimum and maximum displayed pixel values (display range) to be the same as the current image's minimum and maximum pixel values. With 8-bit images, sets the display range to 0-255. With RGB images, does nothing. I usually do "Enhance Contrast", which actually will have over-expose problem, not ideal. I need to check for a 0-1000 range 16-bit image, what's the final 8-bit value will be using resetMinAndMax() - 8bit, or using "Enhance Contrast" - 8 bit

Now, you are ready to dig deeper - familiar with all built-in macro functions and use them!

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