The 3D structure of chromatin plays a key role in genome function, including 
gene expression, DNA replication, chromosome segregation, and DNA repair. 
Furthermore the location of genomic loci within the nucleus, especially relative 
to each other and nuclear structures such as the nuclear envelope and nuclear 
bodies strongly correlates with aspects of function such as gene expression. 
Therefore, determining the 3D position of the 6 billion DNA base pairs in each 
of the 23 chromosomes inside the nucleus of a human cell is a central challenge 
of biology. Recent advances of super-resolution microscopy in principle enable 
the mapping of specific molecular features with nanometer precision inside 
cells. Combined with highly specific, sensitive and multiplexed fluorescence 
labeling of DNA sequences this opens up the possibility of mapping the 3D path 
of the genome sequence in situ. Here we develop computational methodologies to 
reconstruct the sequence configuration of all human chromosomes in the nucleus 
from a super-resolution image of a set of fluorescent in situ probes hybridized 
to the genome in a cell. To test our approach, we develop a method for the 
simulation of DNA in an idealized human nucleus. Our reconstruction method, 
ChromoTrace, uses suffix trees to assign a known linear ordering of in situ 
probes on the genome to an unknown set of 3D in-situ probe positions in the 
nucleus from super-resolved images using the known genomic probe spacing as a 
set of physical distance constraints between probes. We find that ChromoTrace 
can assign the 3D positions of the majority of loci with high accuracy and 
reasonable sensitivity to specific genome sequences. By simulating appropriate 
spatial resolution, label multiplexing and noise scenarios we assess our 
algorithms performance. Our study shows that it is feasible to achieve 
genome-wide reconstruction of the 3D DNA path based on super-resolution 
microscopy images.