http://imagej.273.s1.nabble.com/Counting-cells-automatically-on-a-grid-tp3690263p3690267.html
> Thanks for the Quick reply. Thanks it looks like a good place to
> to Mask, Invert LUT and Watershed. Where will I find them in the menu
Yet another amazing feature of ImageJ ... using the "Plugins >
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
>
> 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