Mice emit ultrasonic vocalizations (USVs) that communicate socially relevant information. To detect and classify these USVs, here we describe VocalMat. VocalMat is a software that uses image-processing and differential geometry approaches to detect U...
Despite recent improvements in microscope technologies, segmenting and tracking cells in three-dimensional time-lapse images (3D + T images) to extract their dynamic positions and activities remains a considerable bottleneck in the field. We develope...
Multiple brain regions are able to learn and express temporal sequences, and this functionality is an essential component of learning and memory. We propose a substrate for such representations via a network model that learns and recalls discrete seq...
Automated detection of complex animal behaviors remains a challenging problem in neuroscience, particularly for behaviors that consist of disparate sequential motions. Grooming is a prototypical stereotyped behavior that is often used as an endopheno...
Forests provide biodiversity, ecosystem, and economic services. Information on individual trees is important for understanding forest ecosystems but obtaining individual-level data at broad scales is challenging due to the costs and logistics of data...
Determining the etiologic basis of the mutations that are responsible for cancer is one of the fundamental challenges in modern cancer research. Different mutational processes induce different types of DNA mutations, providing 'mutational signatures'...
We have developed an open-source software called bi-channel image registration and deep-learning segmentation (BIRDS) for the mapping and analysis of 3D microscopy data and applied this to the mouse brain. The BIRDS pipeline includes image preprocess...
The immunological synapse (IS) is a cell-cell junction between a T cell and a professional antigen-presenting cell. Since the IS formation is a critical step for the initiation of an antigen-specific immune response, various live-cell imaging techniq...
Single-molecule Förster Resonance energy transfer (smFRET) is an adaptable method for studying the structure and dynamics of biomolecules. The development of high throughput methodologies and the growth of commercial instrumentation have outpaced the...