http://imagej.273.s1.nabble.com/Cell-counting-with-imageJ-tp3690375p3690383.html
Esteban: I think ITCN uses a process somewhat more complex than watershed.
that are very close together, and even overlapping slightly. As I
understand, it uses the colvolution and find maxima functions instead. It
results than I ever managed using thresholding and watershed processing. It
launch ITCN. Also, optimize the input parameters with a smaller ROI--if your
On Fri, Nov 13, 2009 at 9:46 AM, G. Esteban Fernandez <
> You can also use the the built-in functions under Analyze > Analyze
> Particles to count automatically after thresholding the images. If
> thresholding doesn't do a good job of including all the nuclei and
> excluding background then it can get tricky. Good thresholding is the
> key to good results with automatic counting. Also, if there are
> nuclei touching each other you can separate them with Process > Binary
> > Watershed. Maybe the ITCN plugin does the separation automatically?
>
> -Esteban
>
>
> On Fri, Nov 13, 2009 at 8:36 AM, Jason Bailey <
[hidden email]>
> wrote:
> > 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> >>>
> >>> (573)882-4895
> >>> (573)884-9676 fax
> >>>
> >>>
> >
>
>
>
> --
> 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>
> (573)882-4895
> (573)884-9676 fax
>