ij-macro-programming-workshop
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:
- Create a tmp image by scaling down the current image by
1/factor, using bilinear interpolation - Apply the
Huangauto-threshold (set the threshold and convert to a mask). - Fill holes to avoid wrong separations by the following watershed
- Run the binary watershed.
- Create a new tmp image by scaling the small image up by
factorusing bilinear interpolation - Apply the
Huangauto-threshold (because of the interpolation the image is not a mask anymore) - Reset the roi-manager
- Use the particle analyzer to detect the nuclei and to add them to the roi-manager
- Close the tmp-images
- 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");
run("Convert to Mask");
run("Fill Holes");
run("Watershed");
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!");
