Analyze set of images giving system parameters

I am fairly new to all of this- but is there a way I can give ImagJ parameters and then have it analyze a group of photos given those parameters? For example, if I have 144 photos of a plant growing over time and I need to measure marked distances on the plant, if I draw a line between the marks on one image, am I able to have imagJ analyze distances for my images having it keep the line ends where I put them?


No worries! I will add a bunch of helpful ‘Getting Started with ImageJ’ links below. But what you really want to do - and will have to do in ImageJ - is write a small macro script. One that will process image after image - but also be interactive - as I’m assuming you need to manually mark the points to measure between?

Here is an example script (based on a template available via the Script Editor at Templates > ImageJ 1.x > Batch > Process Folder (IJ1 Macro)) that I just quickly modified as an example:

 * Macro template to process multiple images in a folder

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

// See also for a version of this code
// in the Python scripting language.


// function to scan folders/subfolders/files to find files with correct suffix
function processFolder(input) {
	list = getFileList(input);
	list = Array.sort(list);
	for (i = 0; i < list.length; i++) {
		if(File.isDirectory(input + File.separator + list[i]))
			processFolder(input + File.separator + list[i]);
		if(endsWith(list[i], suffix))
			processFile(input, output, list[i]);
	// once all images have been gone through - measure line ROIs
	roiManager("Measure"); // measure on original image
	//saves results for all images in a single file
	saveAs("Results", output + "/All_Results.csv"); 

function processFile(input, output, file) {
	run("Bio-Formats", "open=[" + input + "/" + file +"] autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
	waitForUser("Draw your line using the straight line tool and press 't' to add it to the ROI Manager.\nClick 'OK' when finished.");

NOTE: Fiji is Just ImageJ - it is simply a distribution of ImageJ that comes with a bunch of plugins bundled - ready for you to use out-of-the-box. If you are just getting started, we recommend downloading/using Fiji.