
I need help counting dots generated using the paintbrush tool in ImageJ. I tracked dendritic spine formation and spine loss on neurons using the color coded dots across a series of time lapse images. For analysis, I stacked these images so I could align them. I would like to automate the counting of these colored dots to quickly analyze the numbers in excel. The brush width is 5 pixels. I've been playing around and have this much:
lower = 100;
upper = 150;
green = 0;
red = 0;
yellow = 0;
black = 0;
other = 0;
for (y = 0; y < getHeight; y++) {
for (x = 0; x < getWidth; x++) {
v = getPixel(x,y);
r = (v>>16)&0xff; // extract red byte (bits 23-17)
g = (v>>8)&0xff; // extract green byte (bits 15-8)
b = v&0xff; // extract blue byte (bits 7-0)
if (r > upper && g > upper && b < lower) yellow++;
else if (r < lower && g > upper && b < lower) green++;
else if (r > upper && g < lower && b < lower) red++;
else if (r < lower && g < lower && b < lower) black++;
else other++;
}
}
I checked using the same macro, if the brush width is 5 pixels it turns out to return 21 pixels/dot. It would also be helpful if the numbers could automatically be populated into excel. Thanks for the help!