Images should now be sorted based on their time, if "t"+number is a part of...

open("d:/Scratch Assay/Images/5.2.2025 fibroblasty/mit1_t24.JPG");

open("d:/Scratch Assay/Images/5.2.2025 fibroblasty/mit1_t48.JPG");

open("d:/Scratch Assay/Images/2025-03-05 KER/25_1_t48.JPG");

open("d:/Scratch Assay/Images/2025-03-05 KER/25_1_t5.JPG");

open("d:/Scratch Assay/Images/2025-03-05 KER/25_1_t0.JPG");

open("d:/Scratch Assay/Images/2025-03-05 KER/25_1_t24.JPG");

*/

// Parameters that can be adjusted by user to fit to their processing  pipeline.

substringIdentifyingImageGroup = "";  // Should a group of images be pre-selected? If yes, specify a substring that is contained in each of their names.

substringsIdentifyingFirstImage = newArray("t0", "start");  // If an image whose name contains one of these substrings is found, it will be suggested as the starting one.

timeSpecificationPrefix = "t";  // The prefix after which one or more digits specify the time point at which the image was taken. For example, if timeSpecificationPrefix == "time", then "time48h" would be a validtime specification with the value of "48".

substringsIdentifyingFirstImage = newArray("start");  // If an image whose name contains one of these substrings is found, it will be suggested as the starting one.

//substringsIdentifyingFirstImage = newArray(timeSpecificationPrefix + "0", "start");  // If an image whose name contains one of these substrings is found, it will be suggested as the starting one.

// Thresholding method to apply to the gradient image to identify the empty areas. So far, "Minimum" seems to work best.

thresholdingMethodToUse = "Minimum";

limitEmptyROIByExactEmptyRegionsFromFirstImage = !true;  // False if some movement or growth of the gap is allowed (use "Rectangle Between Fiducials From First Image" for limiting the ROI). True if the gap can never move or grow (use "Empty Regions Between Fiducials From First Image").

alwaysCloseOlderIntermediateImagesOnStart = true;

defaultCloseIntermediateImages = true;

}

function createCopyOfImageListWithPaddedTimes(list) {

	listWithPaddedTimes = Array.copy(list);

	// Find how many digits there are in the longest time specification.

	maxDigits = 0;

	for (i = 0; i < listWithPaddedTimes.length; i++) {

		timeSpecification = replace(listWithPaddedTimes[i], ".*" + timeSpecificationPrefix + "(\\d+).*", "$1");

		maxDigits = maxOf(maxDigits, timeSpecification.length);	

	}

	// Zero-pad all time specifications from the left.

	for (i = 0; i < listWithPaddedTimes.length; i++) {

		beforeTimeSpecification = replace(listWithPaddedTimes[i], "(.*" + timeSpecificationPrefix + ")\\d+.*", "$1");

		timeSpecification = replace(listWithPaddedTimes[i], ".*" + timeSpecificationPrefix + "(\\d+).*", "$1");

		afterTimeSpecification = replace(listWithPaddedTimes[i], ".*" + timeSpecificationPrefix + "\\d+(.*)", "$1");

		listWithPaddedTimes[i] = beforeTimeSpecification + String.pad(timeSpecification, maxDigits) + afterTimeSpecification;

	}

	return listWithPaddedTimes;

}

// Setup dialog.

function createSetupDialog() {

	// Get the list of open images. Do not include our own intermediate images, histograms, or plots.

			imageList = Array.concat(imageList, rawImageList[i]);

		}

	}

	if (imageList.length <= 0) {

		showMessage("ERROR: No images open",

		            "No images that could be processed are open, unable to proceed.");

		exit;

	}

	// Sort the list of the image names based on a version where time specifications are zero-padded from the left.

	imageListWithPaddedTimes = createCopyOfImageListWithPaddedTimes(imageList);

	Array.sort(imageListWithPaddedTimes, imageList);

	Dialog.createNonBlocking("Scratch Assay");

	Dialog.addMessage("You will know the process is done when \"All computations done.\"\nmessage appears in the Log window, and an audio tone plays.");

	// Add a list for the selection of the first image. Pre-select the first image whose title contains any of the substrings listed in substringsIdentifyingFirstImage.

	candidateFirstImageTitle = "";

	for (i = 0; i < imageList.length; i++) {

	for (i = 0; (i < imageList.length) && (candidateFirstImageTitle == ""); i++) {

		lowerCaseImageName = toLowerCase(imageList[i]);

		for (j = 0; j < substringsIdentifyingFirstImage.length; j++) {

			if (lowerCaseImageName.indexOf(substringsIdentifyingFirstImage[j]) >= 0) {

		}

	}

	Dialog.setInsets(30, 0, 0);

	Dialog.addImageChoice("Starting image:", candidateFirstImageTitle);

	Dialog.addChoice("Starting image:", imageList, candidateFirstImageTitle)

	Dialog.setInsets(10, 0, 0);

function readSettingsFromSetupDialog() {

	firstImageTitle = Dialog.getImageChoice();

	firstImageTitle = Dialog.getChoice();

	// Determine which images should be analyzed based on the individual checkboxes.

	for (i = 0; i < imageList.length; i++) {

		}

	}

	// Make sure the starting image is the first element of imagesToAnalyze.

	imagesToAnalyze = Array.concat(firstImageTitle, Array.deleteValue(imagesToAnalyze, firstImageTitle));

	// Print out which images will be analyzed.

	print("These images were selected for analysis:" );

	for (i = 0; i < imagesToAnalyze.length; i++) {

function processImages(imagesToAnalyze) {

	// Make sure the starting image is the first element of imagesToAnalyze.

	for (i = 1; i < imagesToAnalyze.length; i++) {

		if (imagesToAnalyze[i] == firstImageTitle) {

			temp = imagesToAnalyze[0];

			imagesToAnalyze[0] = imagesToAnalyze[i];

			imagesToAnalyze[i] = temp;

		}

	} 	

	//setBatchMode("hide");  // TODO: Batch mode can be enabled if no intermediate images should be shown. (However, this might hide the causes of some errors from the user.)

	selectIfExists("Log");

	selectWindow(imageToAnalyzeTitle);

	run("Select None");

	print("\n\n=== Analyzing image \"" + imageToAnalyzeTitle + "\". ===");	

	print("\n\n=== Analyzing image " + (imageIndex+1) + " out of " + imagesToAnalyze.length + ", \"" + imageToAnalyzeTitle + "\". ===");	

	// Create a greyscale copy of the image.

	greyscaleImageToAnalyzeTitle = intermediateDebugImagePrefix + "Grey" + "_" + imageToAnalyzeTitle;

	substringsIdentifyingFirstImage[i] = toLowerCase(substringsIdentifyingFirstImage[i]);

}

createSetupDialog();

readSettingsFromSetupDialog();

originalSelectionColor = Roi.getDefaultColor;