Quantify average signal intensity of Skeletal Muscle fibers

Hi all,

I am trying to quantify the average intensity of different skeletal muscle fibers. I have hard time with thresholding the image without loosing parts of the fibers or having several fibers become one fiber. I have another image I can use to border the fibers, but I do not now how to make it happen. I am new to ImageJ and would appreciate any help.

Attached are the two images.


1 Like

Welcome to the forum, @Lazybones!

So, the trick is to use your border-friendly image to generate a mask, from which you have ROIs, which you can then apply to your original image and measure.

Here is a quick macro I made using the Macro Recorder:

home = call("java.lang.System.getProperty", "user.home");
open(home + "/Desktop/18.1_Terminal Cancer_1-250_puro_2B-2A-lam_20X_Alexa 647.JPG");
setThreshold(0, 10);
run("Create Mask");
run("Fill Holes");
run("Analyze Particles...", "size=1000-Infinity exclude add");
open(home + "/Desktop/18.1_Terminal Cancer_1-250_puro_2B-2A-lam_20X_Alexa 546.JPG");
roiManager("Show All");
run("Set Measurements...", "area mean standard modal min centroid center perimeter bounding fit shape feret's integrated median skewness kurtosis area_fraction stack redirect=None decimal=3");

It assumes your images are saved in your home directory’s Desktop folder.

For details on how I did this, see the Segmentation page.

I leave it as an exercise to the reader how to fix the erroneously large cell #24. :wink: