Posted by
Gabriel Lapointe-2 on
Dec 01, 2009; 1:23am
URL: http://imagej.273.s1.nabble.com/Counting-cells-automatically-on-a-grid-tp3690263p3690264.html
Hi Phil,
Here is the output of the macro recorder on how I counted the algae in
your picture. Actually you don't need any extra plugins for it (using
1.43l). I hope it will gives you pointer on how to avoid manual
counting.
selectWindow("Count 1.JPG");
run("8-bit");
// Many option exist for automatic thresholding, make sure you always
//use the same to be able to compare between images.
setAutoThreshold("MaxEntropy");
setThreshold(0, 126);
// you could use the particle analyzer here but I always find that
// smoothing the edge with binary operation always give better results
run("Convert to Mask");
run("Invert LUT");
run("Invert");
run("Close-");
run("Open");
//separate touching cells
run("Watershed");
// The actual counting
run("Analyze Particles...", "size=35-219 circularity=0.80-1.00
show=Masks exclude include summarize");
Good luck
Gabriel
Gabriel Lapointe, M.Sc.
Laboratoire de Luc DesGroseillers, Ph.D.
Pavillon Roger-Gaudry Local A-538
Département de biochimie
Faculté de Médecine de l'Université de Montréal
2900 boul. Édouard-Montpetit,
Montréal, Qc, H3T 1J4
> Hi everyone,
>
> I am new to ImageJ and it looks like a very powerful tool. I am growing
> algae and need to perform cell counts to determine the cell density
> every day. I would like to reduce the time it takes to do this as
> currently I am doing it manually. I understand that there are plugins
> available which can help me count the cells but I have not had much
> luck. What can you recommend for automated cell counting, are there any
> tutorials available?
>
> One of the problems I have encountered is that the grid interferes with
> the count.
>
> Here is an example of an image that I want to process:
>
http://dl.dropbox.com/u/419501/Count%201.JPG>
> Cheers
>
> Phil