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During development, morphogen gradients precisely determine the position of gene expression boundaries despite the inevitable presence of fluctuations. Recent experiments suggest that some morphogen gradients may be interpreted prior to…
Nowadays, computer-aided sperm analysis (CASA) systems have made a big leap in extracting the characteristics of spermatozoa for studies or measuring human fertility. The first step in sperm characteristics analysis is sperm detection in…
The morphology of retinal blood vessels can indicate various diseases in the human body, and researchers have been working on automatic scanning and segmentation of retinal images to aid diagnosis. This project compares the performance of…
The health and function of tissue rely on its vasculature network to provide reliable blood perfusion. Volumetric imaging approaches, such as multiphoton microscopy, are able to generate detailed 3D images of blood vessels that could…
Automated in-vitro cell detection and counting have been a key theme for artificial and intelligent biological analysis such as biopsy, drug analysis and decease diagnosis. Along with the rapid development of microfluidics and lab-on-chip…
The recent discovery of the striking sheet-like multicellular choanoflagellate species $Choanoeca~flexa$ that dynamically interconverts between two hemispherical forms of opposite orientation raises fundamental questions in cell and…
While recent advances in deep learning have significantly advanced the state of the art for vessel detection in color fundus (CF) images, the success for detecting vessels in fluorescein angiography (FA) has been stymied due to the lack of…
Identification and manipulation of different GABAergic interneuron classes in the behaving animal are important to understand their role in circuit dynamics and behavior. The combination of optogenetics and large-scale neuronal recordings…
Synonymous sites are generally assumed to be subject to weak selective constraint. For this reason, they are often neglected as a possible source of important functional variation. We use site frequency spectra from deep population…
Understanding and extracting the patterns of microscopy images has been a major challenge in the biomedical field. Although trained scientists can locate the proteins of interest within a human cell, this procedure is not efficient and…
Endoscopic images are used at various stages of rectal cancer treatment starting from cancer screening, diagnosis, during treatment to assess response and toxicity from treatments such as colitis, and at follow up to detect new tumor or…
An in-vitro cell culture system is used for biological discoveries and hypothesis-driven research on a particular cell type to understand mechanistic or test pharmaceutical drugs. Conventional in-vitro cultures have been applied to primary…
Reliable large-scale cell detection and segmentation is the fundamental first step to understanding biological processes in the brain. The ability to phenotype cells at scale can accelerate preclinical drug evaluation and system-level brain…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…
It is crucial to measure position and conformational changes of a membrane-interacting protein relative to the membrane surface. This is however challenging because the thickness of a membrane is usually only about 4 nm. We developed a…
Fluorescence spectroscopy and modeling provide powerful means to characterize biomacromolecular structures, dynamics, and interactions. F\"orster resonance energy transfer serves as a key technique for this due to its nanometer-scale…
Accurately predicting individual neurons' responses and spatial functional properties in complex visual tasks remains a key challenge in understanding neural computation. Existing whole-brain connectome models of Drosophila often rely on…
Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further enables one to potentially quantitate relevant parameters to determine the…
A three-dimensional cell culture called a spheroid serves as a foundational entity in a wide variety of modern tissue engineering applications, including 3D-bioprinting and preclinical drug testing. Lack of oxygen within tissue spheroids…