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Detection of MRI brain contour using isotropic and anisotropic diffusion filter. A comparative study.

Reconstructed brain surface from MRI are still based on either interactive or manual edge detection methods which are time consuming and subjective. In order to overcome such inadequate result, the scale-space technique was applied using isotropic and anisotropic diffusion filter. Isotropic diffusion was not adequate because it did not allow locally adaptive blurring. On the contrary, stopping the anisotropic diffusion process at the best time of diffusion, edge detector provided the true location and morphology of the sulci and gyri. Although some sulci appeared open curves this one didn't have to be considered as failure of anisotropic diffusion because it was related to the resolution of the original MR image. Nevertheless the human vision subjectively made explicit their closure.

Anisotropy↗

MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets.

The mammalian genome is organized into large-scale chromosome territories, compartments, domains, and at the smallest scale, chromatin loops and stripes. The newest element is a chromatin jet, a diffused line perpendicular to the main diagonal in the Hi-C contact map, which was reported in quiescent mammalian lymphocytes supporting a two-sided symmetric cohesin loop extrusion model. A similar structure is observed in Repli-HiC data, where relatively thin and straight chromatin fountains indicate coupling of DNA replication forks. However, the precise biological implications of these jet-like structures are unknown due to the limitations in computational methods. We developed MIA-Jet, a multi-scale ridge detection algorithm that can accurately detect jets of variable lengths, widths, and angles. When tested on Hi-C, Repli-HiC, ChIA-PET, ChIA-Drop, and Micro-C data in mouse, human, roundworm, and zebrafish cells, MIA-Jet outperformed existing methods. In human cells, jets were enriched in cohesin loading sites and early replication initiation zones. Applying MIA-Jet to Hi-C data generated from protein-degraded cells revealed that jets are dependent on cohesin but not YY1, and jet signals are strengthened after depleting WAPL. We envision MIA-Jet to be broadly applicable to any 3D genome mapping data, thereby providing new insights into the functional roles of chromatin jets.

3D genome mapping↗