Re: Plugin for selectively counting different cell types in 1 picture?

Posted by BenTupper on
URL: http://imagej.273.s1.nabble.com/Plugin-for-selectively-counting-different-cell-types-in-1-picture-tp5001080p5001082.html

Hi,


On Dec 9, 2012, at 5:02 PM, Daniel Arsen wrote:

> Dear all
>
> I would like to use ImageJ to count phytoplankton cells. My problem is that
> in my samples there are 5 different species of different morphology, and I
> want to count cell numbers per species.
>
> My pictures look like this:
> http://imageshack.us/photo/my-images/707/41514.jpg/
>
> So far, I only found plugins to count different cell types by clicking on
> them (cell counter plugin), or to count all cells in the photo independent
> of their shape (like ITCN and some more plugins). Are there plugins
> available which automatically count a specific cell type, which can be
> predefined by the user?
> Or would I need to write my own Java plugins? Or do you recommend me the use
> of any other software?
>

Philippe Grosjean has lead a project to develop an extensive set of tools for plankton image analysis and classification using ImageJ and R.  You might want to check out what is available here: http://www.sciviews.org/zooimage/   Don't be disappointed with the name, there is a wrapper called PhytoImage for all of the sunlight harvesters out there.

Cheers,
Ben

> In my experiments 320 of these pictures will be generated per day. And
> (compared to the photo above) cell density is going to increase a lot during
> the experiment → cell counting by hand is definitely not an option.
>
> Can you give me a hint for a good plugin?
>
> Thank you for your help!
>
> D.A.
>
>
>
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