The paper presents a pipeline called ICE (Iterative Correction and Eigenvector decomposition) for processing and analyzing Hi-C data to reveal the organization of chromosomes. The pipeline includes read alignment, classification, and iterative correction to eliminate systematic biases, ensuring equal visibility for all genomic regions. The corrected maps are then decomposed into eigenvectors, which provide insights into local chromatin states, global patterns of chromosomal interactions, and the conserved organization of human and mouse chromosomes. The method is validated using published Hi-C datasets and demonstrates improved correlation between different restriction enzymes and between datasets. The eigenvector analysis reveals that the first eigenvector, $E^1$, captures inter-chromosomal interaction preferences related to genomic sequence and local epigenetic states, while the second and third eigenvectors, $E^2$ and $E^3$, capture arm-level organization. The study also shows evolutionary conservation of chromosome organization between human and mouse genomes.The paper presents a pipeline called ICE (Iterative Correction and Eigenvector decomposition) for processing and analyzing Hi-C data to reveal the organization of chromosomes. The pipeline includes read alignment, classification, and iterative correction to eliminate systematic biases, ensuring equal visibility for all genomic regions. The corrected maps are then decomposed into eigenvectors, which provide insights into local chromatin states, global patterns of chromosomal interactions, and the conserved organization of human and mouse chromosomes. The method is validated using published Hi-C datasets and demonstrates improved correlation between different restriction enzymes and between datasets. The eigenvector analysis reveals that the first eigenvector, $E^1$, captures inter-chromosomal interaction preferences related to genomic sequence and local epigenetic states, while the second and third eigenvectors, $E^2$ and $E^3$, capture arm-level organization. The study also shows evolutionary conservation of chromosome organization between human and mouse genomes.