ij-macro-programming-workshop

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Exercise 16.1 - Separate nuclei by using a binary watershed

Aim:

• learn how to separate objects touching each other

The nuclei in the images in the folder images/16 need to be analyzed. However when simply using a threshold and the particle analyzer, the nuclei will not be separtated from each other.

Implement the follwoing protocol in the macro below:

1. Create a tmp image by scaling down the current image by 1/factor, using bilinear interpolation
2. Apply the Huang auto-threshold (set the threshold and convert to a mask).
3. Fill holes to avoid wrong separations by the following watershed
4. Run the binary watershed.
5. Create a new tmp image by scaling the small image up by factor using bilinear interpolation
6. Apply the Huang auto-threshold (because of the interpolation the image is not a mask anymore)
7. Reset the roi-manager
8. Use the particle analyzer to detect the nuclei and to add them to the roi-manager
9. Close the tmp-images
10. Display the rois in the roi-manager on the input image

Your code starts after this line

SCALE_FACTOR = 3;
run("Scale...", "x="+(1.0/SCALE_FACTOR)+" y="+(1.0/SCALE_FACTOR)+" interpolation=Bilinear create title=small_tmp");
setAutoThreshold("Huang dark");

// Convert the image to a mask with the run command - This is the same as pressing the apply button on the Threshold-Adjuster

// Run the fill holes menu command 

// Run the watershed menu command 

run("Scale...", "x="+SCALE_FACTOR+" y="+SCALE_FACTOR+" interpolation=Bilinear create title=big_tmp");
setAutoThreshold("Huang");
roiManager("Reset");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing exclude add");
selectWindow("small_tmp");
close();
selectWindow("big_tmp");
close();
roiManager("Show All");

Your code ends before this line

The code below is for automatically checking the result. Please ignore it!

ok = (nImages>0);
ok = ok && roiManager("count")>2;
if (ok)
	showMessage("That's right. Great, you did it!");
else 
	showMessage("Your result is wrong! Please check your macro and try again!");

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