ImageJ Documentation Wiki

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======Introduction=======
Often image datasets and automated analysis algorithms do not work together as the user would like.  Human-in-the-loop approaches seek to remedy this problem by placing human (in this case the user) into the automated analysis loop.  In order to facilitate robust quantitative analysis of particles such as cancer cell colonies in a 3D matrix by selecting those particles in focus and eliminating out of focus particles, I developed the following pair of macros.  

======Authors========
William J. Ashby  william.j.ashby@vanderbilt.edu  (starting late August 2012, I will have an Auburn University email and likely not have the vanderbilt.edu email)

======Features=======
The first macro, HumanInLoop ParticleAnalysis MeFirst.ijm, runs the batch analysis on a folder of individual images and saves the output in a manner useable by the second macro, HumanInLoop ParticleAnalysis MeLast.ijm.  

The second macro inserts the user into the analysis by reading in the analyzed data and enabling the user to select the particles they want to include in their final analysis.  When selected a red box appears around the particles.  Particles can be unselected by right-clicking, and the box will turn black.  The selected particles are output in a text file containing the filename, list number which is used to keep track of the individual particle, and area of the particle.  Additionally the original spreadsheet "ZZ Results.xls" found in the results folder is amended to contain a column with the heading "Focused" and saved as "Results With Focus Info.xls" in the parent directory.  A value of 1 in this "Focused" column indicates that the  particle was selected.  Simply sorting the spreadsheet using this list will facilitate elimination of the unselected particles.

This macro is provided in beta format since I do not currently have time to develop it further.  I recommend testing it against a small dataset to verify proper functionality before moving to a large dataset.  Please contact me if you identify improper behavior or fix it yourself and amend the code in the wiki accordingly.

=======Installation======
Simply save the two macros as ".txt" of ".ijm" files on your computer.  This can be done with by pasting into a word processor and saving in the appropriate plain text format.   Then run one followed by the other using FIJI.  I would expect them to work in ImageJ but have not tested them in ImageJ.

**Macro 1: HumanInLoop ParticleAnalysis MeFirst.ijm**

<code java>

  //HumanInLoop ParticleAnalysis MeFirst.ijm
  //This macro was designed to facilitate particle analysis of a folder of images by automating the processing of the images in the folder.  It is designed to work with the HumanInLoop ParticleAnalysis MeLast.ijm macro which then facilitates manual selection of desired particles by the user.
//Images to be analyzed should be placed in one directory (Source Directory)
//A second directory should be created to save results files and images (Destination Directory)
//Setting correct Lower and Upper thresholds is important to obtain a good result.

// Developed by William J Ashby.
// Vanderbilt University.

//This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.


  //get appropriate directories from user
  dir1 = getDirectory("Choose Source Directory ");
  dir2 = getDirectory("Choose Destination directory");
  list = getFileList(dir1);

	//give user an opportunity to adjust default parameters to better fit their application
	Dialog.create("Adjust for objective magnification");
	Dialog.addNumber("Objective Magnification (use 10 if unknown)", 10);
	Dialog.addMessage("\tIf needed particle size limits can be adjusted below \nLeave mag. at 10 if customizing particle size limits\n");
	Dialog.addNumber("Minimum particle size (pixels^2)",10000);
	Dialog.addNumber("Maximum particle size (pixels^2)",1000000);
   	Dialog.addMessage("\tIn the following dialogs select \n first the Source Directory, \nthen a Destinaion directory for Results");
   	Dialog.show(); 	

	//Assigning the entered values to variables   
	magnification=Dialog.getNumber();
	userMin=Dialog.getNumber();
	userMax=Dialog.getNumber();
	sMin=magnification*magnification/100*userMin;
	sMax=magnification*magnification/100*userMax;

setBatchMode(true);
    
for (i=0; i<list.length; i++){
	//print (list[i]);
	open(dir1+list[i]);
	name=File.nameWithoutExtension;
	//Prepare the image by removing any scale and making 8-bit
	run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
	run("8-bit");
	saveAs("Tiff", dir2+i+" Original "+name);//Saving with this naming scheme is required for the MeLast macro to function
	//Threshold
	setAutoThreshold("Default");
	run("Convert to Mask");
	//Dilate to close little openings in spheres
	run("Dilate");
	run("Dilate");
	//Analyze particles
	run("Analyze Particles...", "size="+sMin+"-"+sMax+" circularity=0.00-1.00 show=[Count Masks] display exclude include summarize");
	//Save the masks file
	saveAs("Tiff", dir2+i+" CountMask "+name);//Saving with this naming scheme is required for the MeLast macro to function
	close();
	//Save the thresholded image
	saveAs("Tiff", dir2+i+" Thresholded "+name);//Saving with this naming scheme is required for the MeLast macro to function
	
}
//Save the results
selectWindow("Results");
saveAs("Results", dir2+"ZZ Results.xls");

//Save the summary
selectWindow("Summary");
saveAs("Text", dir2+"Z Summary.txt");

</code>


**Macro 2: HumanInLoop ParticleAnalysis MeLast.ijm**

<code java>

  //HumanInLoop ParticleAnalysis MeLast.ijm
  //This macro was designed to facilitate particle analysis of a folder of images by being run after automatically processing  the images in a folder using the HumanInLoop ParticleAnalysis MeFirst.ijm macro.  It facilitates manual selection of desired particles by the user.  Selected images are surrounded by a red box.  Right-clicking removes the particle from those selected and turns the box black.
//The results directory needs to be the same as the results directory used with HumanInLoop ParticleAnalysis MeFirst.ijm
//The macro also asks for the parent directory which contains both the original data directory and the results directory.
//A brief text file will be saved with only the selected particles, their areas, and their filenames.  The original spreadsheet of all the particles will be amended and saved as "Results With Focus Info.xls".  This spreadsheet indicates selected particles by a value of 1 in the column labelled "Focused".  

// Developed by William J Ashby.
// Vanderbilt University.

//This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

//Values for different Cursor Loc input
      shift=1;
      ctrl=2; 
      rightButton=4;
      alt=8;
      leftButton=16;

//Ask user for the previous Results directory
  dir1 = getDirectory("Choose Results Directory ");
//Ask user for the parent directory which should contain both the original data folder and results folder 
  dir2 = getDirectory("Choose Parent Directory ");
  
  list = getFileList(dir1);
//This Text window creates the list matching the numbers to filenames and is essential to making sense of the excel data file
  run("Text Window...","name=Filenames"); 
  print("[Filenames]","Filename\tNumber\tArea\n");

//check that a results list is included
  open(dir1+"ZZ Results.xls");

  print("Number of items in list "+list.length);

for (i=0; i<list.length-2; i=i+3){
	print("Now on list number "+i);
	open(dir1+list[i+1]);
	myImage=File.name;
	run("8-bit");
	open(dir1+list[i]);
	print(File.name);
	rename("CountMask");
	

//Crop image using the mask
	//duplicate the count mask then 
	run("Duplicate...","title=cropMask");
	//make regular mask from count masks
	run("8-bit");
	run("Auto Threshold", "method=Default white");
	//Create extra space in order to see the edges
	for(ii=0; ii<30; ii++)
		run("Erode");
	run("Divide...", "value=255");
	setMinAndMax(0, 1);
	//Crop the original image
	imageCalculator("Multiply", myImage, "cropMask");

	rename("2Display");
	run("RGB Color");
	//Show the cropped image
	
//Ask for user to select focused spheres
      x2=-1; y2=-1; z2=-1; flags2=-1;
      setLineWidth(6);
      xNew=0;
      yNew=0;
      logOpened = false;
      
      print("Click particles you want to keep in your analysis\nClose Log Window to Move to NEXT IMAGE");
      selectWindow("2Display");
      if (getVersion>="1.37r")
          setOption("DisablePopupMenu", true);
      while (!logOpened || isOpen("Log")) {
          getCursorLoc(x, y, z, flags);
          if (x!=x2 || y!=y2 || z!=z2 || flags!=flags2) {
		//lookup the value at x,y, in the count mask
		if (flags&leftButton!=0) {
			selectWindow("CountMask");
			xyVal=getPixel(x,y);
			//If non-zero the get the related data
			if(xyVal!=0){
				xNew=x;
				yNew=y;
				valNew=xyVal-1;
				selectWindow("2Display");
				setColor(255,0,0);
				drawRect(getResult("BX", valNew),getResult("BY", valNew), getResult("Width", valNew), getResult("Height", valNew));
///				//Get the data
				setResult("Focused",valNew, 1);
				print("Getting "+xyVal);
				print("[Filenames]",myImage+"\t"+xyVal+"\t"+getResult("Area",valNew)+"\n");			
			}
			selectWindow("2Display");
			print("Close Log Window to Move to NEXT IMAGE");
		}
		if (flags&rightButton!=0) {
			selectWindow("CountMask");
			print("Close Log Window to Move to NEXT IMAGE");
			xyVal=getPixel(x,y);
			valNew=xyVal-1;
			selectWindow("2Display");
			setColor(0,0,0);
			drawRect(getResult("BX", valNew),getResult("BY", valNew), getResult("Width", valNew), getResult("Height", valNew));
///			//Remove xyVal from data list
			setResult("Focused",valNew, 0);
			print("Removing "+xyVal);
		}
		logOpened = true;
              	startTime = getTime();
          }
          x2=x; y2=y; z2=z; flags2=flags;
          wait(5);
     } //Closing the log window proceeds to next image

     run("Close All");
	
}//end of for loop for processing images in directory

selectWindow("Results");
saveAs("Results", dir2+"Results With Focus Info.xls");

selectWindow("Filenames");
saveAs("Text",dir2+"Filenames and numbers");

</code>