9 research outputs found
Tracking Single-Cells in Overcrowded Bacterial Colonies
No full textCell tracking enables data extraction from timelapse "cell movies" and promotes modeling biological processes at the single-cell level. We introduce a new fully automated computational strategy to track accurately cells across frames in time-lapse movies. Our method is based on a dynamic neighborhoods formation and matching approach, inspired by motion estimation algorithms for video compression. Moreover, it exploits "divide and conquer" opportunities to solve effectively the challenging cells tracking problem in overcrowded bacterial colonies. Using cell movies generated by different labs we demonstrate that the accuracy of the proposed method remains very high (exceeds 97%) even when analyzing large overcrowded microbial colonies
Reconstructing the forest of lineage trees of diverse bacterial communities using bio-inspired image analysis
No full textAnalytics and visualization tools to characterize single-cell stochasticity using bacterial single-cell movie cytometry data
No full textBackground: Time-lapse microscopy live-cell imaging is essential for studying the evolution of bacterial communities at single-cell resolution. It allows capturing detailed information about the morphology, gene expression, and spatial characteristics of individual cells at every time instance of the imaging experiment. The image analysis of bacterial “single-cell movies” (videos) generates big data in the form of multidimensional time series of measured bacterial attributes. If properly analyzed, these datasets can help us decipher the bacterial communities’ growth dynamics and identify the sources and potential functional role of intra- and inter-subpopulation heterogeneity. Recent research has highlighted the importance of investigating the role of biological “noise” in gene regulation, cell growth, cell division, etc. Single-cell analytics of complex single-cell movie datasets, capturing the interaction of multiple micro-colonies with thousands of cells, can shed light on essential phenomena for human health, such as the competition of pathogens and benign microbiome cells, the emergence of dormant cells (”persisters”), the formation of biofilms under different stress conditions, etc. However, highly accurate and automated bacterial bioimage analysis and single-cell analytics methods remain elusive, even though they are required before we can routinely exploit the plethora of data that single-cell movies generate. Results: We present visualization and single-cell analytics using R (ViSCAR), a set of methods and corresponding functions, to visually explore and correlate single-cell attributes generated from the image processing of complex bacterial single-cell movies. They can be used to model and visualize the spatiotemporal evolution of attributes at different levels of the microbial community organization (i.e., cell population, colony, generation, etc.), to discover possible epigenetic information transfer across cell generations, infer mathematical and statistical models describing various stochastic phenomena (e.g., cell growth, cell division), and even identify and auto-correct errors introduced unavoidably during the bioimage analysis of a dense movie with thousands of overcrowded cells in the microscope’s field of view. Conclusions: ViSCAR empowers researchers to capture and characterize the stochasticity, uncover the mechanisms leading to cellular phenotypes of interest, and decipher a large heterogeneous microbial communities’ dynamic behavior. ViSCAR source code is available from GitLab at
Bacterial Image Analysis and Single-Cell Analytics to Decipher the Behavior of Large Microbial Communities
No full textMonitoring individual cell death using time-lapse microscopy: Application to stochastic modeling of microbial inactivation
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Facial expression and gesture analysis for emotionally-rich man-machine interaction
No full textThis chapter presents a holistic approach to emotion modeling and analysis
and their applications in Man-Machine Interaction applications. Beginning
from a symbolic representation of human emotions found in this context,
based on their expression via facial expressions and hand gestures, we
show that it is possible to transform quantitative feature information from
video sequences to an estimation of a user’s emotional state. While these
features can be used for simple representation purposes, in our approach
they are utilized to provide feedback on the users’ emotional state, hoping
to provide next-generation interfaces that are able to recognize the
emotional states of their users
Additional file 1 of Analytics and visualization tools to characterize single-cell stochasticity using bacterial single-cell movie cytometry data
No full textAdditional file 1: Supplementary Informatio
