updated week 3 macro code

Author: Olivier Burri

Week-03/Image Math - Global Operations.ijm

@@ -42,6 +42,7 @@ for(i=0; i<operations.length; i++) {
 
 	// Convert to 32-bit to perform proper image math
 	run("32-bit");
+	// Set the zoom to make the image a bit larger
 	run("In [+]");
 
 	// Running the actual mathematical operation

Week-03/Image_Resizing.ijm

@@ -30,19 +30,20 @@ modifiedBy10	= downUpScale (ori_blobs_ID , 10)	;
 run("Tile");
 waitForUser("From the 'blobs' image we created 'degraded' versions by downscaling and upscaling without interpolation.");
 
-// make a stak from the different images
+// make a stack from the different images
 run("Images to Stack", "method=[Copy (top-left)] name=Stack title=[] use"); 
+waitForUser("The images are now re-arranged as a Stack.\nDue to downscaling and upscaling, the images have different widths and heights.\nThis is why the bottom and right edges have pixels at 0 in some slices");
 // as an alternative you can use method=[Copy (Center)].
-// due to downscaling and upscaling the images have different width and height
+// 
 // the results would then be different
 
-// here we make a line. by defining the point
+// here we make a line. by defining the start and end points
 makeLine(75, 100, 90, 130);
-waitForUser("The images are now re-arranged as a Stack.\nWe also made a line on the image, not let's plot it.")
+waitForUser("We also made a line on the image,\nand we will plot the intentities along that line.")
 
 // and here we ask for the plot.
 run("Plot Profile");
-waitForUser("In the 'Plot' window, click on 'Live'.\nNow, move in the stack using the slider to compare the profiles.\nYou can also move the line by selecting points");
+waitForUser("In the 'Plot' window, click on 'Live'.\nNow, move in the stack using the slider to compare the profiles.\nYou can also move or modify the line by click-dragging its anchor points");
 
 // To continue you can have a look to the CurveFittingDemo :  https://imagej.net/ij/macros/examples/CurveFittingDemo.txt
 // that makes use of Fit functions :  https://imagej.net/ij/developer/macro/functions.html#Fit

Week-03/Ratio Demo Analysis Macro.ijm

@@ -13,6 +13,7 @@
  * 2018 - Olivier Burri, EPFL - SV - BIOP
  * https://biop.epfl.ch
  */
+ 
 run("Close All");
 waitForUser("Please Open 'Ratio Demo Image_Cleaned.tif'\nand press OK.");
 // Use Batch Mode to avoid showing intermediate steps
@@ -62,9 +63,7 @@ setLocation(200, 200);
 // Create a Scale Bar to Go With the Image
 newImage("Scale 0 to 5.0", "32-bit ramp", 256, 20, 1);
 run("6 shades");
-
-
-// Make it Vertical
+// and make it Vertical
 run("Rotate 90 Degrees Left");
 
 // The Ramp 32 bit image goes from 0 to 1 so we multiply it by 5 so it matches our image scale

Week-03/Stack Illumination Correction Demo.ijm

@@ -13,24 +13,44 @@
  * https://biop.epfl.ch
  */
 
-run("Close All");
-waitForUser("Please open the file Worm-Bad-Illumination.tif\nThen press OK");
+ 
+
+ if(!isOpen("worm-bad-illumination.tif") ) {
+	run("Close All");
+	// Ask for file using dialog to open it
+	image = File.openDialog("Please Select the file 'worm-bad-illumination.tif'");
+	open(image);
+
+}
+
+// Make sure the right image is selected
+selectImage("worm-bad-illumination.tif");
+	
+// Build a dialog to ask for the normalization method
+methods = newArray("Min-Max", "Mean");
+
+Dialog.create("Normalization Methods");
+Dialog.addChoice("Method to apply", methods, methods[0]);
+Dialog.addNumber("Provide the new mean value that will be given to each slice of the stack", 10000);
+Dialog.show();
+
+the_method = Dialog.getChoice();
+new_mean = Dialog.getNumber();
 
 // Getting the imasge title helps us rename the image neatly later on in the code
 imageName = getTitle();
 
-newMean = getNumber("Provide the new mean value that will be given to each slice of the stack", 10000);
-
 // Get the siye of the stack through getDimensions()
 getDimensions(x,y,c,z,t);
 
 // Before performing any operation, we duplicate the image in order to avoid losing the original
 // We also rename it, so we know what was done to it
-run("Duplicate...", "duplicate title=["+imageName+"-Corrected]");
+run("Duplicate...", "duplicate title=["+imageName+"-Corrected "+the_method+"]");
 
 // Conversion to 32-bits is very important when performing mathematical operations
 run("32-bit");
 
+
 // We will now go through each timepoint and
 for(i=1; i<t+1;i++) {
 
@@ -42,44 +62,22 @@ for(i=1; i<t+1;i++) {
 
 	// This print to the log window is not necessary, but shows the user something is happening
 	print(area, mean, min, max);
-	
-	// Formula: each pixel has a new value 
-	// newVal = (val - min) / (max - min) * newMean
-	
-	run("Subtract...", "value="+min+" slice");
-	run("Divide...", "value="+(max-min)+" slice");
-	run("Multiply...", "value="+newMean+" slice");
+	if (the_method == "Min-Max") {
+		// Formula: each pixel has a new value 
+		// newVal = (val - min) / (max - min) * newMean
+		
+		run("Subtract...", "value="+min+" slice");
+		run("Divide...", "value="+(max-min)+" slice");
+		run("Multiply...", "value="+new_mean+" slice");
+	} else {
+		run("Divide...", "value="+(mean)+" slice");
+		run("Multiply...", "value="+new_mean+" slice");
+	}
 }
 
 // we ensure that the image is viewable
-setMinAndMax(0, newMean*2);
+setMinAndMax(0, new_mean*2);
 
-// Second Method using only the mean of each slice
-selectImage(imageName);
-// We also rename it, so we know what was done to it
-run("Duplicate...", "duplicate title=["+imageName+"-Corrected v2]");
-
-// Conversion to 32-bits is very important when performing mathematical operations
-run("32-bit");
-
-// We will now go through each timepoint and
-for(i=1; i<t+1;i++) {
-
-	
-	Stack.setFrame(i);
-	
-	getStatistics(area, mean, min, max);
-
-	// This print to the log window is not necessary, but shows the user something is happening
-	print(area, mean, min, max);
-	
-	// Formula: each pixel has a new value 
-	// newVal = Val / mean * newMean
-	
-	run("Divide...", "value="+(mean)+" slice");
-	run("Multiply...", "value="+newMean+" slice");
-}
-setMinAndMax(0, newMean*2);
 run("Tile");
 
 waitForUser("Observe the original and modified images and interpret what you see");