Scripting with Fiji

Why are scripts useful?

They facilitate reproducible science:

  • Document your work
  • Automate your analysis
  • Share with the world

Macro Recorder

1. Launch the Recorder

  • Use the Command Finder! (Ctrl+L)
  • OR: click the Dev icon, then Record...
  • OR: Plugins ▶ Macros ▶ Record...

2. Execute operations

Use the Command Finder (Ctrl+L)!

  • Open sample images
    • Download/unpack "images/C3-jw-30min.zip"
    • Plugins ▶ Bio-Formats ▶ Bio-Formats Importer
    • Open "C3-jw-30min 5_c5.tif"
  • Apply Gaussian blur
  • Apply a threshold (Shift+T)
  • Create Mask
  • Watershed
  • Analyze Particles...
    • Size: 200-Infinity
    • Exclude on edges; Add to Manager

3. Spruce it up

Script Editor

  • Comments
  • Variables
  • Functions
  • String manipulation
  • Conditionals
  • Loops

Batch processing

Process ▶ Batch ▶ Macro...

Templates ▶ ImageJ 1.x ▶ Examples ▶ Process Folder (IJ1 Macro)

Example script to count nuclei in multiple images in a folder/subfolders:


// @File(label = "Input directory", style = "directory") input
// @File(label = "Output directory", style = "directory") output
// @String(label = "File suffix", value = ".tif") suffix

/*
* Macro to count nuclei in multiple images in a folder/subfolders.
*/
	
processFolder(input);
	
// function to scan folders/subfolders/files to find files with correct suffix
function processFolder(input) {
	list = getFileList(input);
	for (i = 0; i < list.length; i++) {
		if(File.isDirectory(input + list[i]))
			processFolder("" + input + list[i]);
		if(endsWith(list[i], suffix))
			processFile(input, output, list[i]);
	}
	//saves results for all images in a single file
	saveAs("Results", output + "/All_Results.tsv"); 
}

function processFile(input, output, file) {
	setBatchMode(true); // prevents image windows from opening while the script is running
	// open image using Bio-Formats
	run("Bio-Formats", "open=[" + input + "/" + file +"] autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
  id = getImageID(); // get original image id
	run("Duplicate...", " "); // duplicate original image and work on the copy
	
	// create binary image
	run("Gaussian Blur...", "sigma=2");
	setAutoThreshold("Default dark");
	//run("Threshold...");
	run("Create Mask");
	run("Watershed");
	// save current binary image
	save(output + "/Binary_OUTPUT_" + file);
	
	run("Analyze Particles...", "size=200-Infinity exclude add");
  selectImage(id); // activate original image
  roiManager("Show All with labels"); // overlay ROIs
	roiManager("Deselect");
	roiManager("Measure"); // measure on original image
	
	// save ROIs for current image
	roiManager("Deselect");
	roiManager("Save", output+ "/" + file + "_ROI.zip"); // saves Rois zip file
	roiManager("Deselect");
	roiManager("Delete"); // clear ROI Manager for next image
}
					

Script parameters

  • Templates ▶ Intro ▶ Widgets (JavaScript)
  • Run
  • Fix the bugs!
  • To the boundedInteger parameter, add:
    style="scroll bar"
  • To the string parameter, add:
    choices={"quick fox", "lazy dog"}
  • Run again

Macros

Comments


// Comments allow you to put human-readable thoughts
// into your code.

// The goal of this "macro" is simply to teach you about comments!

// Comments help you to remember why you did something:
// Set the value to "2" because my boss said so!
value = 2; // Comments can be added to any line!

// Code can be disabled by commenting it out:
// x = y * 2;
					

Variables


// what sorts of values can we assign?
title = "Hello, World!";                // string
intensity = 255;                        // number
a = exp(x * sin(y)) + atan(x * y – a);  // expression

// string constant vs. variable name
text = "title"; 
text = title;

x = 3;
y = x;
x = 5; // what is the value of y after this?

// the variable is assigned after the expression is evaluated
intensity = intensity * 2;
					

Functions


print("Hello, world!");

// functions can return values
// Hint: use parameters instead of calling getNumber
number = getNumber("Type in a number!", 5);

// the "run" function is the most important one
run("Duplicate...", "title=New");

// for arguments with spaces, enclose in square brackets
run("Duplicate...", "title=[with spaces]");
					
Built-in Macro Functions

Strings


name = "copy";

// you can concatenate strings, and strings and numbers
text = "The name is " + name;

// what happens when we run this?
run("Duplicate...", "title=name");

// what's different with this line?
run("Duplicate...", "title=" + name);
					

Conditionals


// @String instructor

if (getBoolean("Is " + instructor + " going too fast?")) {
    hint = "Tell them to to slow down!";
}
else {
    hint = "Try to modify the code, play with it...";
}
showMessage("Advice:", hint);
					

Loops


// For loops:
// They use assignment, test, increment
// Use when you know the # of times the loop will run
for (i = 1; i <= 10; i++) {
    print("Counter: " + i);
}

// While loops:
// Use when you do not necessarily know the # of times the loop will run
while (getBoolean("Do you want me to keep going?")) {
    print("Ok, I'm still going...");
}
showMessage("Ok, I'm done!");
					

Tying it all together

Do you notice a bug in this code?


// this example makes a stack of blurred versions of the
// current slice with a range of radii.

radius = getNumber("Maximal radius?", 5);

title = "Blurred stack of " + getTitle();
run("Duplicate...", "title=[" + title + "]");
run("Select All");
run("Copy");
for (i = 1; i <= radius; i++) {
        run("Add Slice");
        run("Paste");
        run("Gaussian Blur...", "radius=" + radius);
}
					

Further reading

Help from the community—ImageJ forum!

Scripting guide:

Additional workshops and presentations: