biostudies-literatureLamberti WFNational Institutes of HealthNational Institute of General Medical Sciences3387-3398https://www.ebi.ac.uk/biostudies/studies/S-EPMC9260447biostudies-literatureUnknown20Higher-order chromatin structures have functional impacts on gene regulation and cell identity determination. Using high-throughput sequencing (HTS)-based methods like Hi-C, active or inactive compartments and open or closed topologically associating domain (TAD) structures can be identified on a cell population level. Recently developed high-resolution three-dimensional (3D) molecular imaging techniques such as 3D electron microscopy with in situ hybridization (3D-EMSIH) and 3D structured illumination microscopy (3D-SIM) enable direct detection of physical representations of chromatin structures in a single cell. However, computational analysis of 3D image data with explainability and interpretability on functional characteristics of chromatin structures is still challenging. We developedComputational and structural biotechnology journalExtracting physical characteristics of higher-order chromatin structures from 3D image data.PMC9260447R35GM133712Lamberti WFZang CfalseExtracting physical characteristics of higher-order chromatin structures from 3D image data.Higher-order chromatin structures have functional impacts on gene regulation and cell identity determination. Using high-throughput sequencing (HTS)-based methods like Hi-C, active or inactive compartments and open or closed topologically associating domain (TAD) structures can be identified on a cell population level. Recently developed high-resolution three-dimensional (3D) molecular imaging techniques such as 3D electron microscopy with in situ hybridization (3D-EMSIH) and 3D structured illumination microscopy (3D-SIM) enable direct detection of physical representations of chromatin structures in a single cell. However, computational analysis of 3D image data with explainability and interpretability on functional characteristics of chromatin structures is still challenging. We developed2022-01-01T00:00:00Z20222025-04-04T03:06:08.073Z2025-04-04T03:06:08.073ZS-EPMC92604473583263310.1016/j.csbj.2022.06.018