IEEE transactions on pattern analysis and machine intelligence
29993708
We present a method combining affinity prediction with region agglomeration, which improves significantly upon the state of the art of neuron segmentation from electron microscopy (EM) in accuracy and scalability. Our method consists of a 3D U-Net, t...
IEEE transactions on image processing : a publication of the IEEE Signal Processing Society
30028701
In this paper, we propose a novel contour-seed pairs learning-based framework for robust and automated cell/nucleus segmentation. Automated granular object segmentation in microscopy images has significant clinical importance for pathology grading of...
Proceedings of the National Academy of Sciences of the United States of America
30509984
Novelty detection is a fundamental biological problem that organisms must solve to determine whether a given stimulus departs from those previously experienced. In computer science, this problem is solved efficiently using a data structure called a B...
MOTIVATION: Recognition of different genomic signals and regions (GSRs) in DNA is crucial for understanding genome organization, gene regulation, and gene function, which in turn generate better genome and gene annotations. Although many methods have...
Genes to cells : devoted to molecular & cellular mechanisms
31095815
Dendrites of neurons receive and process synaptic or sensory inputs. The Drosophila class IV dendritic arborization (da) neuron is an established model system to explore molecular mechanisms of dendrite morphogenesis. The total number of dendritic br...
Genomes are organized into self-interacting chromatin regions called topologically associated domains (TADs). A significant number of TAD boundaries are shared across multiple cell types and conserved across species. Disruption of TAD boundaries may ...
Reverse engineering of gene regulatory networks (GRNs) is a central task in systems biology. Most of the existing methods for GRN inference rely on gene co-expression analysis or TF-target binding information, where the determination of co-expression...
IEEE/ACM transactions on computational biology and bioinformatics
31425122
With the rise of image-based transcriptomics, spatial gene expression data has become increasingly important for understanding gene regulations from the tissue level down to the cell level. Especially, the gene expression images of Drosophila embryos...