http://imagej.273.s1.nabble.com/Counting-cells-automatically-on-a-grid-tp3690263p3690266.html
Thanks for the Quick reply. Thanks it looks like a good place to start.
to Mask, Invert LUT and Watershed. Where will I find them in the menu
> 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