Added contrast enhancement to the empty region detection. Applied "keep only... (fea52317) · Commits · cbia / ScratchAssay

ScratchAssay.ijm

+42 −7

Original line number	Original line	Diff line number	Diff line
	@@ -18,6 +18,16 @@ open("d:/Scratch Assay/Images/2025-03-05 KER/25_1_t24.JPG");



			*/

			/*

			TODO: (General TODO notes.)

			In the first image of a series, try to pick only the one largest component (assume the gap is unbroken in the first image).

			In each subsequent image, try intersection of empty regions from that image with a dilated version of the empty regions from the previous image (dilation radius as a parameter linked to cell size).

	*/		*/


	@@ -243,9 +253,13 @@ function readSettingsFromSetupDialog() {
	firstImageTitle = Dialog.getChoice();		firstImageTitle = Dialog.getChoice();

	// Determine which images should be analyzed based on the individual checkboxes.		// Determine which images should be analyzed based on the individual checkboxes.
			firstImageTitleFound = false;
	for (i = 0; i < imageList.length; i++) {		for (i = 0; i < imageList.length; i++) {
	if (Dialog.getCheckbox()) {		if (Dialog.getCheckbox()) {
	imagesToAnalyze = Array.concat(imagesToAnalyze, imageList[i]);		imagesToAnalyze = Array.concat(imagesToAnalyze, imageList[i]);
			if (imageList[i] == firstImageTitle) {
			firstImageTitleFound = true;
			}
	}		}
	}		}

	@@ -262,11 +276,13 @@ function readSettingsFromSetupDialog() {
	}		}
	}		}

	// Make sure the starting image is the first element of imagesToAnalyze.		// If firstImageTitle was found among the images to process, make sure it is the first element of imagesToAnalyze.
			if (firstImageTitleFound) {
	imagesToAnalyze = Array.concat(firstImageTitle, Array.deleteValue(imagesToAnalyze, firstImageTitle));		imagesToAnalyze = Array.concat(firstImageTitle, Array.deleteValue(imagesToAnalyze, firstImageTitle));
			}

	// Print out which images will be analyzed.		// Print out which images will be analyzed.
	print("These images were selected for analysis:" );		print("The images will be analyzed in this order:" );
	for (i = 0; i < imagesToAnalyze.length; i++) {		for (i = 0; i < imagesToAnalyze.length; i++) {
	print(imagesToAnalyze[i]);		print(imagesToAnalyze[i]);
	}		}
	@@ -764,6 +780,15 @@ function processImage(imageIndex, imageToAnalyzeTitle) {
	run("Duplicate...", "title=[" + greyscaleImageToAnalyzeTitle + "]");		run("Duplicate...", "title=[" + greyscaleImageToAnalyzeTitle + "]");
	run("8-bit");		run("8-bit");

			// Try to enhance the contrast of the cells while also smoothing the
			//run("Enhance Contrast...", "saturated=0 normalize");
			//run("Enhance Contrast...", "saturated=5 normalize");
			//run("Enhance Contrast...", "saturated=10 normalize");
			run("Enhance Contrast...", "saturated=20 normalize"); // High values of "saturated" (up to 20 was tested) seem to help with low-contrast images.
			run("Median...", "radius=5"); // TODO: Median radius should be smaller than the cell size. (About one third of the SE size used for morphological gradient/opening seems to work.)
			//waitForUser("");


	// Find the fiducials and the area between them.		// Find the fiducials and the area between them.
	findFiducials(imageIndex, imageToAnalyzeTitle, greyscaleImageToAnalyzeTitle);		findFiducials(imageIndex, imageToAnalyzeTitle, greyscaleImageToAnalyzeTitle);

	@@ -826,7 +851,7 @@ function processImage(imageIndex, imageToAnalyzeTitle) {


	// Calculate the image gradient.		// Calculate the image gradient.
	run("Morphological Filters", "operation=Gradient element=Disk radius=15"); // TODO: Radius should be related to the actual cell diameter in the image. (Version B: morphological gradient)		run("Morphological Filters", "operation=Gradient element=Disk radius=15"); // TODO: Radius should be related to the actual cell diameter in the image.
	gapImageToAnalyzeTitle = intermediateDebugImagePrefix + "Gap" + "_" + imageToAnalyzeTitle;		gapImageToAnalyzeTitle = intermediateDebugImagePrefix + "Gap" + "_" + imageToAnalyzeTitle;
	rename(gapImageToAnalyzeTitle);		rename(gapImageToAnalyzeTitle);

	@@ -844,6 +869,16 @@ function processImage(imageIndex, imageToAnalyzeTitle) {
	run("Convert to Mask");		run("Convert to Mask");
	// Refine the gap mask.		// Refine the gap mask.
	run("Fill Holes (Binary/Gray)");		run("Fill Holes (Binary/Gray)");


			// Morphological opening.
			run("Morphological Filters", "operation=Opening element=Disk radius=15"); // TODO: Radius should be related to the actual cell diameter in the image. Possibly the same value as used for the gradient computation.
			// TODO: Treat the gap mask in the first image of a series differently -- keep only the largest component.
			if (imageIndex == 0) {
			run("Keep Largest Region");
			}


	run("Area Opening", "pixel=15000"); // TODO: The area parameter of this area opening should be related to the actual cell diameter in the image.		run("Area Opening", "pixel=15000"); // TODO: The area parameter of this area opening should be related to the actual cell diameter in the image.
	// Convert the mask into a selection and store it.		// Convert the mask into a selection and store it.
	run("Create Selection");		run("Create Selection");