Biology subjects

Bub, G.

Publications and source records attributed to Bub, G..

10 recordsLinked to original sources

bioRxiv2026

RhythmWriter: GPU-accelerated Contractility Quantification for Large Datasets

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have been considered optimal model systems for use in cardiac safety testing, yet their adoption remains low, largely because of technical limitations in the analysis methodology. RhythmWriter (RW) is an open-source GPU plugin for ImageJ developed to quantify contractile motion over extended periods of time. RW compensates for baseline drift, is time-scale invariant and is capable of very rapid data analysis. As a consequence, RW is capable of generating simultaneous high-resolution contraction restitution curves from multiple aggregates of hiPSC-CMs derived from premature-stimulus (S1S2) and dynamic-ramp restitution protocols. The aggregates exhibit brief refractory periods, which allow the induction of S2 beats at coupling intervals down to 130 ms and 1:1 entrainment during periodic stimulation down to a cycle length of 245 ms. Simulations confirm the ability of RW to track programmed contractile strength and stimulation intervals even at rapid pacing rates. This makes possible, for the first time, high-throughput functional assessment of hiPSC-CM aggregates for contractility drug screening and maturation.

physiology↗

bioRxiv2026

Reinforcement learning discovers new mechanisms of reentry in excitable media

The transition from transient excitation to sustained reentry is a fundamental problem in the physics of excitable media. In cardiac tissue, reentry underlies many life-threatening cardiac arrhythmias, yet the pathway to initiation of reentry remains incompletely understood. Here, we formulate reentry initiation as a reinforcement-learning problem in which an agent applies sequences of spatial stimulation patterns while being rewarded for sustained activity and penalized according to the number of stimuli applied. Using cellular automata in one-, two-, and three-dimensional geometries, the agent discovered several mechanisms for generating unidirectional propagation and reentry. These included a previously described mechanism combining superthreshold and subthreshold stimulation, as well as two new mechanisms based entirely on subthreshold stimuli: a sequential mechanism involving stimuli delivered at different locations and times, and a spatial mechanism in which several individually subthreshold sites collectively initiated reentry. In geometries containing boundaries and branches, the learned protocols additionally exploited structural source-sink asymmetries. Optogenetic experiments in cardiac monolayers further demonstrated reproducible induction of unidirectional propagation using the learned spatial subthreshold patterns, while whole-heart experiments provided preliminary evidence that such patterns can shape early propagation in intact tissue. More broadly, we show that reinforcement learning provides a general framework for discovering mechanisms of reentry in arbitrary geometries and generating testable hypotheses about reentry initiation in excitable systems.

physiology↗

bioRxiv2026

iMyocyte: A Web-Based Cellular Automata Platform for Real-Time Demonstration of Cardiac Reentry

Cardiac arrhythmias arise from excitable-media dynamics that are often challenging to teach and visualize in real time. To address this, we developed iMyocyte, an interactive web-based platform for real-time demonstration of excitation wave propagation, conduction block, and reentry dynamics using a simplified cellular automaton model (i.e., a network of discrete cells that change state based on neighbouring cells). In iMyocyte, a network is built from student devices, each representing a model cell coupled to its neighbours to propagate excitation. Unlike traditional teaching materials, iMyocyte lets students manipulate key model parameters and immediately observe how these shape wave dynamics and reentry conditions. Pilot classroom deployments with undergraduate life science students at McGill University indicate high engagement and suggest improved conceptual clarity, motivating future work to improve the platforms usability, robustness, and visualization features, and to conduct formal learning assessment.

physiology↗

bioRxiv2026

Real-Time GPU-Accelerated Digital Heart Twin: Integrating Bidirectional Interactions Between Living Optogenetic Monolayers and Computational Simulations

Reentrant arrhythmias are life-threatening cardiac events that are difficult to study due to limited experimental control over the complex circuit dynamics. We aimed to develop a real-time digital heart twin that allows in real-time dynamic manipulation of reentrant pathways in vitro using physiologically relevant simulations. We designed a closed-feedback loop system that couples a cultured cardiac monolayer with a two-dimensional computational simulation of cardiac tissue. The simulation, based on GPU-accelerated models (e.g., cellular automata), predicts wave propagation in real-time using the Abubu.js library. Optical mapping captures monolayer activation patterns, and simulation outputs are converted into light-based stimulation via optogenetics, using LEDs and microcontrollers to depolarize cardiac tissue. Our platform is capable of accurately detecting and responding to electrical waves in real-time, enabling interactive control of reentrant circuits. The system replaces traditional fixed-delay stimulation protocols with computationally guided interventions, better mimicking physiological conduction dynamics. This digital twin provides a novel and responsive method to study reentrant arrhythmias. Its integration of optical stimulation, real-time modeling, and tissue feedback enables the construction of user-defined reentry pathways under dynamic control. By merging computational and biological systems, this work introduces a versatile experimental framework for investigating arrhythmias. The platform may inform future control and anti-arrhythmic strategies and pave the way for personalized cardiac electrophysiology studies.

bioengineering↗

bioRxiv2025

Phase resetting in human stem cell derived cardiomyocytes explains complex cardiac arrhythmias

Phase resetting of cardiac oscillators underlies some complex arrhythmias. Here we use optogenetic stimulation to construct phase response curves (PRC) for spheroids of human induced pluripotent stem cell derived cardiomyocytes (iPSC-CM) and a computational cardiomyocyte model to identify ionic mechanisms shaping the PRC. The clinical utility of the human PRCs is demonstrated by adding a patient-based conduction delay to the same equations to explain complex multi-day Holter ECG dynamics and cardiac arrhythmias. Periodic stimulation of these patient-based models and the computational model of human iPSC-CM reveal similar bifurcation patterns and entrainment zones. Cell therapy by injecting iPSC-CM into diseased hearts can induce ectopic foci-based engraftment arrhythmias. The PRC analysis offers a potential strategy to entrain these foci in a parameter space that avoids such arrhythmias.

physiology↗

bioRxiv2024

Automated measurement of cardiomyocyte monolayer contraction using the Exeter Multiscope

We apply a novel microscope architecture, the Exeter Multiscope, to the problem of acquiring image data in rapid succession from nine wells of a 96 well plate. We demonstrate that the new microscope can detect contraction in cardiomyocyte monolayers which have been plated into these wells. Each well is sampled using 500 x 500 pixels across a 1.4 x 1.4 mm field of view, acquired in three colours at 3.7 Hz per well. The use of multiple illumination wavelengths provides post-hoc focus selection, further increasing the level of automation. The performance of the Exeter Multiscope is benchmarked against industry standard methods using a commercial microscope with a motorised stage and demonstrates that the Multiscope can acquire data almost 40 times faster. The data from both Multiscope and the commercial systems are processed by a pixel variance algorithm that uses information from the pixel value variability over time to determine the timing and amplitude of tissue contraction. This algorithm is also benchmarked against an existing algorithm that employs an absolute difference measure of tissue contraction.

biophysics↗

bioRxiv2022

Simultaneous widefield voltage and interferometric dye-free optical mapping quantifies electromechanical waves in human iPSC-cardiomyocytes.

Coupled electro-mechanical waves define hearts function in health and disease. Genetic abnormalities, drug-triggered or acquired pathologies can disrupt and uncouple these waves with potentially lethal consequences. Optical mapping of electrical waves using fluorescent dyes or genetically-encoded sensors in human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs) offers mechanistic insights into cardiac conduction abnormalities. Interferometric dye-free/label-free wave mapping (without specific sensors) presents an alternative, likely capturing the mechanical aspects of cardiac conduction. Because of its non-invasive nature and spectral flexibility (not restricted to a specific excitation wavelength), it is an attractive chronic imaging tool in iPSC-CMs, as part of all-optical high-throughput platforms. In this study, we developed simultaneous widefield voltage and interferometric dye-free optical imaging methodology that was used: 1) to validate dye-free optical mapping for quantification of cardiac wave properties in human iPSC-CMs; 2) to demonstrate low-cost optical mapping of electromechanical waves in hiPSC-CMs using recent near-infrared (NIR) voltage sensors and orders of magnitude cheaper miniature CMOS cameras; 3) to uncover previously underexplored frequency- and space-varying parameters of cardiac electromechanical waves in hiPSC-CMs. We find similarity in the frequency-dependent responses of electrical (NIR fluorescence imaged) and mechanical (dye-free imaged) waves, with the latter being more sensitive to faster rates and showing steeper restitution and earlier appearance of wave-front tortuosity. During regular pacing, the dye-free imaged conduction velocity and the electrical wave velocity are correlated; both modalities being sensitive to pharmacological uncoupling and both dependent on gap-junctional protein (connexins) determinants of wave propagation. We uncover strong frequency-dependence of the electromechanical delay (EMD) locally and globally in hiPSC-CMs on a rigid substrate. The presented framework and results offer new means to track the functional responses of hiPSC-CM inexpensively and non-invasively for counteracting heart disease and aiding cardiotoxicity testing and drug development.

bioengineering↗

bioRxiv2020

KHz-rate volumetric voltage imaging of the whole zebrafish heart

Fast volumetric imaging is essential for understanding the function of excitable tissues such as those found in the brain and heart. Measuring cardiac voltage transients in tissue volumes with spatial and temporal resolutions needed to give insight to cardiac function has so far been impossible. We introduce a new imaging modality based on simultaneous illumination of multiple planes in the tissue and parallel detection with multiple cameras, avoiding compromises inherent in any scanning approach. The system enables imaging of voltage transients in-situ, allowing us, for the first time, to map voltage activity in the whole heart volume at KHz rates. The unprecedented spatio-temporal resolution of our method enabled the observation of novel dynamics of electrical propagation through the zebrafish atrioventricular canal.

physiology↗

bioRxiv2019

Optical interrogation of sympathetic neuronal effects on macroscopic cardiac monolayer dynamics

Alterations in autonomic function are known to occur in cardiac conditions including sudden cardiac death. Cardiac stimulation via sympathetic neurons can potentially trigger arrhythmias. Dissecting direct neural-cardiac interactions at the cellular level is technically challenging and understudied due to the lack of experimental model systems and methodologies. Here we demonstrate the utility of optical interrogation of sympathetic neurons and their effects on macroscopic cardiac monolayer dynamics to address research targets such as the effects of adrenergic stimulation via the release of neurotransmitters, the effect of neuronal numbers on cardiac wave behaviour and the applicability of optogenetics in mechanistic in vitro studies. We combine photo-uncaging or optogenetic neural stimulation with imaging of cardiac monolayers to measure electrical activity in an automated fashion, illustrating the power and high throughput capability of such interrogations. The methods described highlight the challenges and benefits of co-cultures as experimental model systems.

biophysics↗

bioRxiv2019

Solid State High Throughput Screening Microscopy

We introduce a solid state high throughput screening (ssHTS) imaging modality that uses a novel Newtonian telescope design to image multiple spatially separated samples without moving parts or robotics. Conventional high-throughput imaging modalities either require movement of the sample to the focal plane of the imaging system1-3 or movement of the imaging system itself4,5, or use a wide-field approach to capture several samples in one frame. Schemes which move the sample or the imaging system can be mechanically complex and are inherently slow, while wide-field imaging systems have poor light collection efficiency and resolution compared to systems that image a single sample at a given time point. Our proposed ssHTS system uses a large parabolic reflector and an imaging lenses positioned at their focal distances above each sample. A fast LED array sequentially illuminate samples to generate images that are captured with a single camera placed at the focal point of the reflector. This optical configuration allows each sample to completely fill a sensors field of view. Since each LED illuminates a single sample and LED switch times are very fast, images from spatially separated samples can be captured at rates limited only by the cameras frame rate. The system is demonstrated by imaging cardiac monolayer and Caenorhabditis elegans (C. elegans) preparations.

bioengineering↗