The 3D folding structure formed by different genomic regions of a chromosome is 
still poorly understood. So far, only relatively simple geometric features, like 
distances and angles between different genomic regions, have been evaluated. 
This work is concerned with more complex geometric properties, i.e., the 
complete shape formed by genomic regions. Our work is based on statistical shape 
theory and we use different approaches to analyze the considered structures, 
e.g., shape uniformity test, 3D point-based registration, Fisher distribution, 
and 3D non-rigid image registration for shape normalization. We have applied 
these approaches to analyze 3D microscopy images of the X-chromosome where four 
consecutive genomic regions (BACs) have been simultaneously labeled by 
multicolor FISH. We have acquired two sets of four consecutive genomic regions 
with an overlap of three regions. From the experimental results, it turned out 
that for all data sets the complete structure is non-random. In addition, we 
found that the shapes of active and inactive X-chromosomal genomic regions are 
statistically independent. Moreover, we reconstructed the average 3D structure 
of chromatin in a small genomic region (below 4 Mb) based on five BACs resulting 
from two overlapping four BAC regions. We found that geometric normalization 
with respect to the nucleus shape based on non-rigid image registration has a 
significant influence on the location of the genomic regions.