Related papers: scellop: A Scalable Redesign of Cell Population Pl…
Image-based or morphological profiling is a rapidly expanding field wherein cells are "profiled" by extracting hundreds to thousands of unbiased, quantitative features from images of cells that have been perturbed by genetic or chemical…
The problem of cell association is considered for cellular users present in the field. This has become a challenging problem with the deployment of 5G networks which will share the sub-6 GHz bands with the legacy 4G networks. Instead of…
The cell cycle duration is a variable cellular phenotype that underlies long-term population growth and age structures. By analyzing the stationary solutions of a branching process with heritable cell division times, we demonstrate…
The recent advances in single-cell technologies have enabled us to profile genomic features at unprecedented resolution and datasets from multiple domains are available, including datasets that profile different types of genomic features…
Understanding the higher-order interactions within network data is a key objective of network science. Surveys of metadata triangles (or patterned 3-cycles in metadata-enriched graphs) are often of interest in this pursuit. In this work, we…
Our work targets automated analysis to quantify the growth dynamics of a population of bacilliform bacteria. We propose an innovative approach to frame-sequence tracking of deformable-cell motion by the automated minimization of a new,…
Coarse-graining microscopic models of biological neural networks to obtain mesoscopic models of neural activities is an essential step towards multi-scale models of the brain. Here, we extend a recent theory for mesoscopic population…
For the Bio+Med-Vis Challenge 2024, we propose a visual analytics system as a redesign for the scatter pie chart visualization of cell type proportions of spatial transcriptomics data. Our design uses three linked views: a view of the…
We have produced a new software package for the simulation of pulsar populations, \textsc{PsrPopPy}, based on the \textsc{Psrpop} package. The codebase has been re-written in Python (save for some external libraries, which remain in their…
Neighborhood graphs and clustering algorithms are fundamental structures in both computational geometry and data analysis. Visualizing them can help build insight into their behavior and properties. The Ipe extensible drawing editor,…
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…
Systems biology is an inter-disciplinary field that studies systems of biological components at different scales, which may be molecules, cells or entire organism. In particular, systems biology methods are applied to understand functional…
The unrelenting increase in the population of mobile users and their traffic demands drive cellular network operators to densify their network infrastructure. Network densification shrinks the footprint of base stations (BSs) and reduces…
Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels,…
Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of…
Graph clustering has many important applications in computing, but due to the increasing sizes of graphs, even traditionally fast clustering methods can be computationally expensive for real-world graphs of interest. Scalability problems…
Modelling, analysing and inferring triggering mechanisms in population reproduction is fundamental in many biological applications. It is also an active and growing research domain in mathematical biology. In this chapter, we review the…
We present an application, Superplot, for calculating and plotting statistical quantities relevant to parameter inference from a "chain" of samples drawn from a parameter space, produced by e.g. MultiNest. A simple graphical interface…
The CellxGene project has enabled access to single-cell data in the scientific community, providing tools for browsed-based no-code analysis of more than 500 annotated datasets. However, single-cell data requires dimensional reduction to…
We introduce a novel method for overlaying cell type proportion data onto tissue images. This approach preserves spatial context while avoiding visual clutter or excessively obscuring the underlying slide. Our proposed technique involves…