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In moving camera videos, motion segmentation is commonly performed using the image plane motion of pixels, or optical flow. However, objects that are at different depths from the camera can exhibit different optical flows even if they share…
This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…
The dispersal of cells from an initially constrained location is a crucial aspect of many physiological phenomena ranging from morphogenesis to tumour spreading. In such processes, the way cell-cell interactions impact the motion of single…
A novel and fast semi-automatic method for segmentation, locating and counting blood cells in an image is proposed. In this method, thresholding is used to separate the nucleus from the other parts. We also use Hough transform for circles…
Despite significant advances in particle imaging technologies over the past two decades, few advances have been made in particle tracking, i.e. linking individual particle positions across time series data. The state-of-the-art tracking…
We introduce and theoretically investigate a minimal particle-based model for a new class of active matter where particles exhibit directional, volume-conserving division in confinement while interacting sterically, mimicking cells in early…
Bacterial colonies can form a wide variety of shapes and structures based on ambient and internal conditions. To help understand the mechanisms that determine the structure of and the diversity within these colonies, various numerical…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…
Contact inhibition limits migration and proliferation of cells in cell colonies. We consider a multiphase field model to investigate the growth dynamics of a cell colony, composed of proliferating cells. The model takes into account the…
Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…
In this paper, we propose an efficient clustering technique to solve the problem of clustering in the presence of obstacles. The proposed algorithm divides the spatial area into rectangular cells. Each cell is associated with statistical…
This paper looks into the problem of pedestrian tracking using a monocular, potentially moving, uncalibrated camera. The pedestrians are located in each frame using a standard human detector, which are then tracked in subsequent frames.…
Superpixel algorithms aim to over-segment the image by grouping pixels that belong to the same object. Many state-of-the-art superpixel algorithms rely on minimizing objective functions to enforce color ho- mogeneity. The optimization is…
Replication time is among the most important components of a bacterial cell's reproductive fitness. Paradoxically, larger cells replicate in less time than smaller cells despite the fact that building a larger cell requires increased…
Multimodal single-cell technologies enable the simultaneous collection of diverse data types from individual cells, enhancing our understanding of cellular states. However, the integration of these datatypes and modeling the…
Learning the continuous dynamics of a system from snapshots of its temporal marginals is a problem which appears throughout natural sciences and machine learning, including in quantum systems, single-cell biological data, and generative…
Event cameras are bioinspired sensors with reaction times in the order of microseconds. This property makes them appealing for use in highly-dynamic computer vision applications. In this work,we explore the limits of this sensing technology…
Single Particle Tracking (SPT) can aid in understanding complex spatio-temporal processes. However, quantifying diffusivity and forces from individual live cell trajectories is complicated by inter- & intra-trajectory kinetic heterogeneity,…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…