subcounting objects

[Paolo Ariano]

Hi all,

i'm trying to count spots in every cells ... so i've two pictures of the
same field of view:

1. the first picture shows the whole cells, so treshold and then analyze
particles and i obtain all the outlines saved and added to the
roi-manager

2. then i open the second image containing a lot of little spots inside
every cells area, now i'd like to count the spots number in every roi
i've in the roi-manager, how to finish the work ?

thanks a lot
paolo
--
NeuroScience PhD
Post-doc @ University of Torino
www.personalweb.unito.it/paolo.ariano
www.cellular-neurophysiology.unito.it
www.mieleria.it

[Gabriel Landini]

On Thursday 18 June 2009  12:27:51 Paolo Ariano wrote:

> i'm trying to count spots in every cells ... so i've two pictures of the
> same field of view:
>
> 1. the first picture shows the whole cells, so treshold and then analyze
> particles and i obtain all the outlines saved and added to the
> roi-manager
>
> 2. then i open the second image containing a lot of little spots inside
> every cells area, now i'd like to count the spots number in every roi
> i've in the roi-manager, how to finish the work ?

If you have the cells as binary objects and the particles to be counted as
"holes" then you can use the ParticleHoleNumber.txt macro in the morphology
collection.

Cheers,

G.

[Paolo Ariano]

Il giorno gio, 18/06/2009 alle 12.31 +0100, Gabriel Landini ha scritto:
> If you have the cells as binary objects and the particles to be counted as
> "holes" then you can use the ParticleHoleNumber.txt macro in the morphology
> collection.

thanks Gabirel,
i'll try but i think it doesn't correlate the single cell/roi with the
numbers of particles inside this cells/roi :(

till next
paolo
--
NeuroScience PhD
Post-doc @ University of Torino
www.personalweb.unito.it/paolo.ariano
www.cellular-neurophysiology.unito.it
www.mieleria.it

[Stoyan Pavlov]

Hi Paolo,
I had similar problem recently. I solved it using the folowing macro. Please
excuse me because I am not really good with the macro language and the macro
is a bit sluggish but it worked for me. You can modify so it is more
appropriate to your needs.Here it is:

// This Macro counts particles inside specific Roi and otputs the number to
TAB separated Log window which after saving can be imported to excel.
        n = roiManager("count");
        for (i=0; i<n; i++)  {
        roiManager("select", i);
         run("Analyze Particles...", "size=2-20 circularity=0.00-1.00
show=Nothing display clear ");
    m=nResults;
        print (i,"    ",":","    ", m) ;

Have a nice day!
Stoyan Pavlov



On Thu, Jun 18, 2009 at 1:39 PM, Paolo Ariano <[hidden email]> wrote:

> Hi all,
>
> i'm trying to count spots in every cells ... so i've two pictures of the
> same field of view:
>
> 1. the first picture shows the whole cells, so treshold and then analyze
> particles and i obtain all the outlines saved and added to the
> roi-manager
>
> 2. then i open the second image containing a lot of little spots inside
> every cells area, now i'd like to count the spots number in every roi
> i've in the roi-manager, how to finish the work ?
>
> thanks a lot
> paolo
> --
> NeuroScience PhD
> Post-doc @ University of Torino
> www.personalweb.unito.it/paolo.ariano
> www.cellular-neurophysiology.unito.it<http://www.personalweb.unito.it/paolo.ariano%0Awww.cellular-neurophysiology.unito.it>
> www.mieleria.it
>

... [show rest of quote]

--
Dr. Stoyan P. Pavlov, MD
Departament of Anatomy, Histology and Embryology
Medical University "Prof. Dr. Paraskev Stoyanov", Varna
Prof. Marin Drinov Str.55
9002 Varna
Bulgaria
Tel: +359 (0) 52 - 677 - 050 #2638
e-mail: [hidden email]

[ashish ram]

Thanks a lot for your help.

On Sun, Jun 21, 2009 at 3:45 AM, Stoyan Pavlov <[hidden email]>wrote:

> Hi Paolo,
> I had similar problem recently. I solved it using the folowing macro.
> Please
> excuse me because I am not really good with the macro language and the
> macro
> is a bit sluggish but it worked for me. You can modify so it is more
> appropriate to your needs.Here it is:
>
> // This Macro counts particles inside specific Roi and otputs the number to
> TAB separated Log window which after saving can be imported to excel.
>        n = roiManager("count");
>        for (i=0; i<n; i++)  {
>        roiManager("select", i);
>         run("Analyze Particles...", "size=2-20 circularity=0.00-1.00
> show=Nothing display clear ");
>    m=nResults;
>        print (i,"    ",":","    ", m) ;
>
> Have a nice day!
> Stoyan Pavlov
>
>
>
> On Thu, Jun 18, 2009 at 1:39 PM, Paolo Ariano <[hidden email]>
> wrote:
>
> > Hi all,
> >
> > i'm trying to count spots in every cells ... so i've two pictures of the
> > same field of view:
> >
> > 1. the first picture shows the whole cells, so treshold and then analyze
> > particles and i obtain all the outlines saved and added to the
> > roi-manager
> >
> > 2. then i open the second image containing a lot of little spots inside
> > every cells area, now i'd like to count the spots number in every roi
> > i've in the roi-manager, how to finish the work ?
> >
> > thanks a lot
> > paolo
> > --
> > NeuroScience PhD
> > Post-doc @ University of Torino
> > www.personalweb.unito.it/paolo.ariano
> > www.cellular-neurophysiology.unito.it<
> http://www.personalweb.unito.it/paolo.ariano%0Awww.cellular-neurophysiology.unito.it
> >
> > www.mieleria.it
> >
>
>
>
> --
> Dr. Stoyan P. Pavlov, MD
> Departament of Anatomy, Histology and Embryology
> Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> Prof. Marin Drinov Str.55
> 9002 Varna
> Bulgaria
> Tel: +359 (0) 52 - 677 - 050 #2638
> e-mail: [hidden email]
>

... [show rest of quote]

[Paolo Ariano]

Il giorno dom, 21/06/2009 alle 01.15 +0300, Stoyan Pavlov ha scritto:
> Hi Paolo,
> I had similar problem recently. I solved it using the folowing macro. Please
> excuse me because I am not really good with the macro language and the macro
> is a bit sluggish but it worked for me. You can modify so it is more
> appropriate to your needs.Here it is:
>
> // This Macro counts particles inside specific Roi and otputs the number to
> TAB separated Log window which after saving can be imported to excel.

thanks a lot Stoyan,
it seems to make the right job, i'll try it in the afternoon :)
till next
paolo
--
NeuroScience PhD
Post-doc @ University of Torino
www.personalweb.unito.it/paolo.ariano
www.cellular-neurophysiology.unito.it
www.mieleria.it