Volume of cluster

[Aaron Johnson-9]

I'm measuring the volume of a cluster of objects (like a cluster of grapes)
in an 8-bit stacked image.  Some clusters are tightly grouped and others are
more spread out.  I can threshold and measure the volume of the components
of the cluster, but I'm having a hard time figuring out how I can measure
the volume of the entire cluster, including the space between the cluster
components.  Is there an automated way to do this?  Can I either fill in the
holes (I've tried Binary:Fill Holes but the holes are too big) or maybe
automatically draw a ROI that encompasses all the cluster components?  Any
advice would be much appreciated.  Thanks.

Aaron

-------------------------
Aaron M. Johnson
Doctoral Student
Dept. of Surgery
University of Wisconsin - Madison

[Robert Dougherty]

Aaron,

You my be able to do something with the 3D Euclidean Distance Transformation
(AKA distance map) or even the local thickness.  The idea would be to
consider a point to be part of the cluster if it is close enough, in some
sense, to a grape point.  This would include some extra volume around the
outside.  Another thought would be a 3D convex hull, but I'm not aware of a
plugin for that.

Bob
 

Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
Phone [phone]
Fax [phone]
www.optinav.com
 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On
> Behalf Of Aaron Johnson
> Sent: Thursday, October 23, 2008 9:12 PM
> To: [hidden email]
> Subject: Volume of cluster
>
>
> I'm measuring the volume of a cluster of objects (like a
> cluster of grapes) in an 8-bit stacked image.  Some clusters
> are tightly grouped and others are more spread out.  I can
> threshold and measure the volume of the components of the
> cluster, but I'm having a hard time figuring out how I can
> measure the volume of the entire cluster, including the space
> between the cluster components.  Is there an automated way to
> do this?  Can I either fill in the holes (I've tried
> Binary:Fill Holes but the holes are too big) or maybe
> automatically draw a ROI that encompasses all the cluster
> components?  Any advice would be much appreciated.  Thanks.
>
> Aaron
>
> -------------------------
> Aaron M. Johnson
> Doctoral Student
> Dept. of Surgery
> University of Wisconsin - Madison
>
>

[Aaron Johnson-9]

Bob, thanks for heading me in the right direction.  The convex hull (2D) is
a possibility, but I think a concave hull would actually work better for my
application.  Does anyone know of a concave hull plugin?
Aaron