Re: Cell counting with imageJ

Posted by Jason Bailey-2 on
URL: http://imagej.273.s1.nabble.com/Cell-counting-with-imageJ-tp3690375p3690381.html

Antonis,

I have had much luck with the Image-Based Tool for Counting Nuclei (ITCN)
with mammalian cells. I imagine it could work well with yours as well. I
typically do two counts--first count all nuclei labeled with Hoechst 33342,
then count the nuclei labeled with a different dye (either ethidium or FITC,
usually). Although this might require some changes to how you label your
cells.

If you must resort to manual counting, the "Cell Counter" plugin marks
cells/nuclei as you click and lets you track multiple cell types as you go.

Both are available at the ImageJ Plugins page:
http://rsbweb.nih.gov/ij/plugins/index.html

Good luck!

Jason

On Fri, Nov 13, 2009 at 9:25 AM, Antonis Giakountis <[hidden email]> wrote:

> Hi Esteban,
>
> I really would prefer not to do it by hand. A typical experiment of mine
> involves several timepoints (10-16) and at least five reps per line. Each
> one of those has hundreds of cells and I was hoping for some stitistics out
> of this. To make a long story sort I expect thousants of cells and I would
> like to get an estimation of the percentage of them that has fluorescence
> out of the total.
>
> In the worst case I could deal with user define-clinking as long as I could
> mark the cells that are counted. As for the images I am aiming for
> triple-stain nuclear immunofluorescence, but since this is done with the
> confocal I can easily scan each channel separately, including the
> transmitted-light one (BF).
>
> Antonis
> ----- Original Message ----- From: "G. Esteban Fernandez" <
> [hidden email]>
>
> To: <[hidden email]>
> Sent: Friday, November 13, 2009 2:10 PM
>
> Subject: Re: Cell counting with imageJ
>
>
>  How many images/cells do you need to count?  Is this something that
>> you can do by hand in a matter of a couple of days or do you want an
>> automated procedure?  Often it takes a few days to get an automated
>> procedure to work correctly, if it ever works at all, during which
>> time you could've done the counting by hand.  There are probably
>> ImageJ plugins that keep track of counts as you click on cells in the
>> images.
>>
>> Do you have images that match the fluorescence images to get total
>> cell numbers?  For example transmitted light (brightfield/phase/DIC)
>> images?
>>
>> -Esteban
>>
>>
>> On Fri, Nov 13, 2009 at 7:43 AM, Antonis Giakountis <[hidden email]>
>> wrote:
>>
>>> Dear all,
>>>
>>> I am a plant Biologist and I would like to use ImageJ in order to count
>>> cell numbers (diameter 10-20 microns on average) and to estimate percentage
>>> of cells that have fluorescence.
>>>
>>> Is it possible to to that with ImageJ and if yes do I have to install a
>>> certain plugin? If not can you recomment another software?
>>>
>>> Thank you in advance for your time,
>>>
>>> Antonis
>>>
>>> --------------------------------------------
>>> Antonis Giakountis, PhD
>>> Prof. David Baulcombe group
>>> Department of Plant Sciences
>>> University of Cambridge
>>> Downing Street
>>> Cambridge CB2 3EA
>>> UK
>>>
>>>
>>
>>
>> --
>> G. Esteban Fernandez, Ph.D.
>>
>> Associate Director
>> Molecular Cytology Core Facility
>> University of Missouri
>> 120 Bond Life Sciences Center
>> Columbia, MO  65211
>>
>> http://www.biotech.missouri.edu/mcc
>>
>> [phone]
>> [phone] fax
>>
>>