Confocal Data For Geometric Morphometric Analysis

Previous Topic Next Topic
classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

Confocal Data For Geometric Morphometric Analysis

Chris Rhodes

Geometric morphometrics involves analysis of shape changes based upon data
from homologous landmarks (corresponding anatomical points from specimens).
I therefore need to obtain the 3D coordinates of specific parts of the image
in the most efficient manner possible.

I've seen discussion of saving X,Y coordinates in the archive, but I need to
save X,Y,Z coordinates if possible.

I have looked at the program, but I might well be missing something that is
obvious to the experienced user.

I have already used the BLJ plugin for volume/surface rendering of Z-stacks
".lsm" files in 3D. I now need to be able to collect quantitative data from
the file.

Thank You


----Original Message Follows----
From: vytas <[hidden email]>
To: [hidden email]
Subject: Re: Morphometrics On Confocal Data
Date: Thu, 04 Aug 2005 09:45:10 -0500

>Hello Chris,

         Re your posting to ImageJ list, perhaps you should be more explicit
about the type of measurements/data you wish to extract and the type of

Vytas Bindokas, Ph.D.
Research Assoc. / Assoc. Prof.,
Director, BSD Light Microscopy Core Facility
Dept Neurobiol Pharmacol Physiol MC0926
947 E 58th Street
The University of Chicago
Chicago IL 60637
Room J246A (SBRI)

fax 773-702-5903
email [hidden email]
  web site for LMCF:



What is the best way to collect 3D landmark data from Z-stacks?

I want to collect data using a Zeiss confocal laser scanning microscope,
which produces ".lsm" files, and perform 3D geometric morphometrics on it.

Please let me know if other software could enhance this process.

Chris Rhodes