Particle Counting in Cells

Hi there,

I have a picture having a lot of cells that engulfed beads (‘particles’) during phagocytosis. Some cells engulfed ten or more beads. Is there a way to count these particles from each individual cell? I have mild experience with ImageJ, so can someone help step-by-step?

Hi
@Dev_Patel
Post a image we can probably help you.
Greeting

Hi @Mathew,

Project_Image014_ch02.tif (1.2 MB) Project_Image014_ch03.tif (1.7 MB)

I have many such pictures to work on. If you know of the way and count particles, can you post up the instructions as well so that I know how to work accordingly with the other pictures I have?

That would be very helpful. Thank you in advance!

Hi @Dev_Patel

I give you the method and not the macro (it’s up to you) :wink:

To identify the cells I will do:
run (“Lab Stack”);
run (“Stack to Images”);
then:
n = roiManager ( “count”)
a loop:
for (i = 0; i <n; i ++)
{
choose an image
roiManager ( “select”, i)
duplicate
find maxima
}

An example for loop

An example for find Maxima

Macro.

img=getImageID();
run("Duplicate...", "title=1");
//setTool("rectangle");
makeRectangle(4, 28, 1336, 950);
run("Duplicate...", "title=2");
run("Duplicate...", "title=3");
getInfo("image.description");
run("Lab Stack");
run("Stack to Images");
selectWindow("b*");
setAutoThreshold("Otsu dark");
//run("Threshold...");
run("Convert to Mask");
run("Watershed");
run("Set Measurements...", "area display redirect=None decimal=2");;
run("Analyze Particles...", "size=1.00-Infinity exclude add");
selectWindow("2");
n=roiManager("count");
{
for(i=0;i<n;i++)
{
selectWindow("L*");
roiManager("select",i);
run("Duplicate...","title="+i);
roiManager("Show None");
//run("Select None");
run("Find Maxima...", "prominence=2 strict exclude output=Count");
j=getResult("Count");
roiManager("Update");
roiManager("Rename", j);
}
run("Tile");

Hi Mathew,

I am a beginner to ImageJ. What does ‘Lab Stack’ reference to? I tried running the macro and a pop-up tells ‘it is undefined’.

I am using the latest version.

Hi @Dev_Patel
read this:
https://imagej.nih.gov/ij/docs/guide/146-28.html#toc-Subsection-28.1
Perform each operation line by line to see.

The macro works for your image:
Project_Image014_ch02.tif

Delete this line
getInfo(“image.description”);