The latest imaging devices are the results of long term developments and there are
several applications for accurate geometric modeling. Apart from macromolecular structure
analyses, application of synchrotron X-ray microtomography (XMT) is a new and promising
area in the biosciences. XMT includes the analysis of images, however, prior to apply
in simulation or in diagnostic intensive research is required. This paper presents
a method, how to obtain information from the recent TOMCAT experimental instrument
(built in 2006), and how to manage its huge amount of image data. Object reconstruction
from biological data has several difficulties and numerous images have to be processed.
The procedure has clinical relevance; the images were taken of neural tissue samples.
These samples are taken by a procedure called micro-punch; the tiny samples are mechanically
cut from specially prepared tissues of the brain. This paper presents a digital-punch
method to extract the valuable information from the noisy images, supporting object
reconstruction applications. The main purpose of this method is to obtain enough data
to create a geometrically accurate and topologically correct vessel network of the