3D particle volume measurement

[Paola Lepanto]

I´m new in image analysis stuff and I´ve been working with confocal
stacks in which I would like to quantify the volume of particles that
have the same fluorescence intensity as cells and in some instances are
in contact with cells. In this cases I´ve been unable to separate the
particles from the cells in the whole stack using segmentation from the
3D object counter. I think I would need to use something like
"watershed" for 3D stacks. Does anybody knows if something like this
exists and how it works or have any other solution? Thanks in advance.
Paola

[Johannes-P. Koch]

There is a plugin from Tom Gniadek called WatershedCounting3D available
under:  http://130.132.232.37/~tjg22/; please cite the paper when using it.
As far as I have used it, it works fine, but - as with almost every
watershed algorithm - you might have to face the problem of
oversegmentation.

Best
Johannes

----- Original Message -----
From: "Paola Lepanto" <[hidden email]>
To: <[hidden email]>
Sent: Wednesday, July 22, 2009 10:28 PM
Subject: 3D particle volume measurement

> I´m new in image analysis stuff and I´ve been working with confocal stacks
> in which I would like to quantify the volume of particles that have the
> same fluorescence intensity as cells and in some instances are in contact
> with cells. In this cases I´ve been unable to separate the particles from
> the cells in the whole stack using segmentation from the 3D object
> counter. I think I would need to use something like "watershed" for 3D
> stacks. Does anybody knows if something like this exists and how it works
> or have any other solution? Thanks in advance.
> Paola
>
>

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