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How to label all objects in a binary image?

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How to label all objects in a binary image?

Daniel James White
Hi Mohanned

try the
Analyze Particles
tool, built into imageJ/Fiji

but first go to
Set Measurements
and tun on the stuff you want to measure

lastly, dont forget to read the imageJ user guide
http://rsbweb.nih.gov/ij/docs/guide/index.html
(its very good!)
 before asking trivial questions!
many answers are right there!

cheers


D

On Nov 20, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote:

> Date:    Sat, 19 Nov 2011 12:07:20 +0200
> From:    Mohammed Tlais <[hidden email]>
> Subject: How to label all objects in a binary image?
>
> Dear All,
>
> I have a binary images of cells, and I want to detect these cells to do my
> measurements (area, perimeter, etc...). Is there any tool for that?
>
> I used to work on a software that has a simple label function to process
> the binary image and copy the label into a labelled image.
>
> Best Regards,
> Moe Tleis

Dr. Daniel James White BSc. (Hons.) PhD

Leader - Image Processing Facility,
Senior Microscopist,
Light Microscopy Facility.

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)
chalkie666 Skype
http://www.bioimagexd.net  BioImageXD
http://fiji.sc                                        Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Biopolis Dresden Imaging Platform (BioDIP)
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )
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Re: How to label all objects in a binary image?

karo03
Hi

to stay with your habits, have a look into the morphology plugins of Gabriel Landini. There is a binary label and binarylabel8

Regards
Karsten

Am 20.11.2011 um 11:04 schrieb daniel white:

> Hi Mohanned
>
> try the
> Analyze Particles
> tool, built into imageJ/Fiji
>
> but first go to
> Set Measurements
> and tun on the stuff you want to measure
>
> lastly, dont forget to read the imageJ user guide
> http://rsbweb.nih.gov/ij/docs/guide/index.html
> (its very good!)
> before asking trivial questions!
> many answers are right there!
>
> cheers
>
>
> D
>
> On Nov 20, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote:
>
>> Date:    Sat, 19 Nov 2011 12:07:20 +0200
>> From:    Mohammed Tlais <[hidden email]>
>> Subject: How to label all objects in a binary image?
>>
>> Dear All,
>>
>> I have a binary images of cells, and I want to detect these cells to do my
>> measurements (area, perimeter, etc...). Is there any tool for that?
>>
>> I used to work on a software that has a simple label function to process
>> the binary image and copy the label into a labelled image.
>>
>> Best Regards,
>> Moe Tleis
>
> Dr. Daniel James White BSc. (Hons.) PhD
>
> Leader - Image Processing Facility,
> Senior Microscopist,
> Light Microscopy Facility.
>
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> +49 (0)15114966933 (German Mobile)
> +49 (0)351 210 2627 (Work phone at MPI-CBG)
> +49 (0)351 210 1078 (Fax MPI-CBG LMF)
> chalkie666 Skype
> http://www.bioimagexd.net  BioImageXD
> http://fiji.sc                                        Fiji -  is just ImageJ (Batteries Included)
> http://www.chalkie.org.uk                Dan's Homepages
> https://ifn.mpi-cbg.de  Biopolis Dresden Imaging Platform (BioDIP)
> dan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )

Karsten
[hidden email]
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Re: How to label all objects in a binary image?

David Webster
To clarify, set the "Show" option from the "Analyze Particles" window to
"Count Masks".
Also works in vanilla ImageJ, you don't need to download Fiji if you
haven't done so already.

David Webster

On Sun, Nov 20, 2011 at 4:17 AM, Karsten <[hidden email]> wrote:

> Hi
>
> to stay with your habits, have a look into the morphology plugins of
> Gabriel Landini. There is a binary label and binarylabel8
>
> Regards
> Karsten
>
> Am 20.11.2011 um 11:04 schrieb daniel white:
>
> > Hi Mohanned
> >
> > try the
> > Analyze Particles
> > tool, built into imageJ/Fiji
> >
> > but first go to
> > Set Measurements
> > and tun on the stuff you want to measure
> >
> > lastly, dont forget to read the imageJ user guide
> > http://rsbweb.nih.gov/ij/docs/guide/index.html
> > (its very good!)
> > before asking trivial questions!
> > many answers are right there!
> >
> > cheers
> >
> >
> > D
> >
> > On Nov 20, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote:
> >
> >> Date:    Sat, 19 Nov 2011 12:07:20 +0200
> >> From:    Mohammed Tlais <[hidden email]>
> >> Subject: How to label all objects in a binary image?
> >>
> >> Dear All,
> >>
> >> I have a binary images of cells, and I want to detect these cells to do
> my
> >> measurements (area, perimeter, etc...). Is there any tool for that?
> >>
> >> I used to work on a software that has a simple label function to process
> >> the binary image and copy the label into a labelled image.
> >>
> >> Best Regards,
> >> Moe Tleis
> >
> > Dr. Daniel James White BSc. (Hons.) PhD
> >
> > Leader - Image Processing Facility,
> > Senior Microscopist,
> > Light Microscopy Facility.
> >
> > Max Planck Institute of Molecular Cell Biology and Genetics
> > Pfotenhauerstrasse 108
> > 01307 DRESDEN
> > Germany
> >
> > +49 (0)15114966933 (German Mobile)
> > +49 (0)351 210 2627 (Work phone at MPI-CBG)
> > +49 (0)351 210 1078 (Fax MPI-CBG LMF)
> > chalkie666                                    Skype
> > http://www.bioimagexd.net     BioImageXD
> > http://fiji.sc                                        Fiji -  is just
> ImageJ (Batteries Included)
> > http://www.chalkie.org.uk             Dan's Homepages
> > https://ifn.mpi-cbg.de                        Biopolis Dresden Imaging
> Platform (BioDIP)
> > dan (at) chalkie.org.uk
> > ( white (at) mpi-cbg.de )
>
> Karsten
> [hidden email]
>