Posted by
Romain Guiet on
Oct 09, 2015; 9:25am
URL: http://imagej.273.s1.nabble.com/Calculate-bubble-volume-tp5014331p5014586.html
Hi Dimitris,
You will find below some suggestions and a macro regarding the measurement of the bubbles’ volume.
1 – image saturation : your image is saturated (and a lot). You should consider to decrease the exposure time of your acquisition. Indeed saturated pixels could be considered as (walking) dead pixels. They do not give any information + they make the detection more difficult and less accurate + they make the processing less robust. So, DO NOT acquire saturated images, please.
2 – Pixel size : what is the minimal size of the bubbles that you would like to quantify ?
Many of them are too small to be accurately detected. I don’t know much about your experiment but if you expect that the tiny bubbles population could change from one condition to another you should adapt your pixel size (objective, c-mount, …).
You will find below a macro (that work not so badly on the precise image you provided), but considering point 1- and 2- , it could be less accurate on a different image.
The macro contains some parameters that you could tune.
Results are in pixel, pixel^2, pixel^3 respectively for radius, area, volume.
Knowing your objective magnification, c-mount, pixel size on the chip of your camera and the binning during the acquisition you should be able to do the math and get the metric values.
Cheers,
Romain
////////////////////////////////////////////////////////////////////////////// start of the macro
/*
* Goal : Measure Volume of bubbles on a 2D image
*
* Strategy : Measure area of each bubble, approximate a radius and calculate a volume
*
* IP Strategy :
* - get seed points, using find maxima on a blured image
* - detect bubbles boundaries, using Level sets with the previously detected seed points
* - analyze particles to keep only the roundish objects
* - from the area, calculate the radius and volume and populate back the result table
*/
////////////////////////////////////////////////////////////////////////////// start of the macro
closeImages = false;
roiManager("Reset");
run("Clear Results");
////////////////////////////////////////////////////////////////////////////// set the measurements
run("Set Measurements...", "area limit display redirect=None decimal=3"); // area, limited to threshold, display label
title = getTitle(); // get the title of the original image to select it later
////////////////////////////////////////////////////////////////////////////// detect the center of the bubbles
run("Duplicate...", "title=gb2"); //
run("Gaussian Blur...", "sigma=2"); // apply a gaussian blur
run("Find Maxima...", "noise=10 output=[Point Selection] light"); // and look for local maxima to retrieve the center, use as seed points at the next step
////////////////////////////////////////////////////////////////////////////// detect bubbles boundaries
selectImage(title); //
run("Duplicate...", "title=med2"); //
run("Median...", "radius=2"); // denoise a bit before using level sets
run("Restore Selection"); // restore the (previously detected) seed points on this image
// and use level sets (you can try different parameters)
run("Level Sets", "method=[Active Contours] use_fast_marching grey_value_threshold=40 distance_threshold=0.30 advection=2.20 propagation=1 curvature=1 grayscale=50 convergence=0.0050 region=outside");
selectImage("Segmentation of med2"); //
run("Invert"); // invert the image (for the analyze particles step)
rename(title+"-mask"); // rename the image so the rows in result table mention the current image analyzed
////////////////////////////////////////////////////////////////////////////// detect roundish particles, calculate radius ...
selectImage(title+"-mask");
run("Analyze Particles...", "size=5-Infinity circularity=0.80-1.00 display add"); // you can change circularity parameters
Vtotal = 0 ;
resultNbr = nResults;
for ( rowIndex = 0 ; rowIndex < resultNbr ; rowIndex++){
area = getResult("Area", rowIndex);
radius = sqrt( area / PI) ;
Volume = 4 * PI * pow(radius,3) / 3 ;
setResult("radius",rowIndex,radius);
setResult("Volume",rowIndex,Volume);
Vtotal = Vtotal + Volume;
}
////////////////////////////////////////////////////////////////////////////// print the total volume
print("Vtotal : "+title+" = "+Vtotal);
////////////////////////////////////////////////////////////////////////////// prepare an ouput image
selectImage(title);
roiManager("Show All without labels");
run("Flatten");
rename(title+"-results");
if (closeImages){
////////////////////////////////////////////////////////////////////////////// close unnecessary images
selectImage("gb2");
close();
selectImage("med2");
close();
selectImage(title+"-mask");
close();
}
////////////////////////////////////////////////////////////////////////////// end of the macro
---------------------------------------------------------------
Dr. Romain Guiet
Bioimaging and Optics Platform (PT-BIOP)
Ecole Polytechnique Fédérale de Lausanne (EPFL)
Faculty of Life Sciences
Station 19, AI 0140
CH-1015 Lausanne
Phone: [+4121 69] 39629
http://biop.epfl.ch/---------------------------------------------------------------
________________________________________
De : ImageJ Interest Group [
[hidden email]] de la part de Dimitris Karampalis [
[hidden email]]
Envoyé : lundi 14 septembre 2015 15:10
À :
[hidden email]
Objet : Calculate bubble volume
Hello all,
I would like to calculate the total volume of the bubbles in pictures like the one that I've attached. Could anyone help me with that please?Thanks in advance for your time.
Dimitris
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