Oct 24, 2024 · Recent advances in chromatin labelling, imaging and automated fluidics technologies have led to the development of chromatin tracing, enabling direct mapping of the 3D chromatin folding...

Jan 31, 2025 · Caption: This image shows the three-dimensional genome structures of several chromosomes reported in a Dip-C study, which were used to train the new ChromoGen model. Credits: ... of genome folding principles and demonstrates that generative AI can bridge genomic and epigenomic features with 3D genome structure, pointing to future work on ...

Why endogenous tagging? The 3D Cell Viewer is a tool for viewing thousands of 3D images of cellular structures and organelles.

Su et al. present a high-throughput, multi-modal imaging platform to assay the 3D organization of chromatin at genome scale in its functional context in thousands of cells.

Nov 13, 2020 · Recent advances in image-based 3D genomics techniques have enabled direct tracing of chromatin folding and multiplexed imaging of nucleome architectures in single cells of several important biological systems. Here, we discuss these advances and the future directions of image-based 3D genomics.

Chromatin tracing is used to visualize the 3D folding path of chromatin, offering insights into genome organization. Chromatin tracing directly visualizes genomic loci in situ, providing a...

Mar 26, 2018 · In this review, we focus on the introduction of novel imaging and visualization methods to study 3D genomes. First, we introduce the progress made recently in 3D genome imaging in both fixed cell and live cells based on long-probe labeling, short-probe labeling, RNA FISH, and the CRISPR system.

Understanding the 3D genome architecture can answer several fundamental biological questions regarding the integration of chromatin packaging patterns with various genomic and epigenomic features. We expect the development of enormous 3D epigenome and transcriptome datasets in …

Oct 1, 2024 · In this review, we summarize the expanding portfolio of 3D genomic technologies, highlighting recent developments and applications from the past three years. Lastly, we present an outlook of where this technology-driven field might be headed.

3D DAPI image The DAPI image process produces a complete 3D morphology image (the morphology.ome.tif output file) for each of the stained regions and determines the reference image volume that cells are segmented from and decoded transcripts are assigned to.