Plugin for selectively counting different cell types in 1 picture?

[Daniel Arsen]

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?

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.

[BenTupper]

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?
>

... [show rest of quote]

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.
>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/Plugin-for-selectively-counting-different-cell-types-in-1-picture-tp5001080.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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[Daniel Arsen]

Ok, thank you very much!!
I will try Zoo/Phyto-Image then