Re: Counting cells automatically on a grid

Posted by Philip Keymer on Dec 01, 2009; 4:37am
URL: http://imagej.273.s1.nabble.com/Counting-cells-automatically-on-a-grid-tp3690263p3690268.html

Hi Ben (and Wayne)

On Mon, 2009-11-30 at 21:37 -0500, Ben Tupper wrote:

> Hi,
>
> On Nov 30, 2009, at 9:19 PM, Philip Keymer wrote:
>
> > Hi Gabriel,
> >
> > Thanks for the Quick reply.  Thanks it looks like a good place to  
> > start.
> > Looking at the Macro I am having trouble finding the options for  
> > Convert
> > to Mask, Invert LUT and Watershed.  Where will I find them in the menu
> > structure?
> >
>
> Yet another amazing feature of ImageJ ... using the "Plugins >  
> Utilities > Find Commands..." menu option you can find the location of  
> the menu command as well as the source code location.  Set the "Show  
> full information" option on for maximum wow.  Is that slick or what?
>
> Cheers,
> Ben
>

Thanks for that Now I will be able to find all the tools which are
mention in the macro and play with the settings.  That is a brilliant
feature for such a complex software package.

>
> > Cheers
> >
> > Phil
> >
> > On Mon, 2009-11-30 at 20:23 -0500, Gabriel Lapointe wrote:
> >> 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
>
>
> Cheers,
> Ben

Cheers,

Phil