FlyNet 2.0: drosophila heart 3D (2D + time) segmentation in optical coherence microscopy images using a convolutional long short-term memory neural network

Matt

et al. 2022

JoVE

Self Cite

Using Drosophila melanogaster (fruit fly) as a model organism has ensured significant progress in many areas of biological science, from cellular organization and genomic investigations to behavioral studies. Due to the accumulated scientific knowledge, in recent years, Drosophila was brought to the field of modeling human diseases, including heart disorders. The presented work describes the experimental system for monitoring and manipulating the heart function in the context of a whole live organism using red light (617 nm) and without invasive procedures. Control over the heart was achieved using optogenetic tools. Optogenetics combines the expression of lightsensitive transgenic opsins and their optical activation to regulate the biological tissue of interest. In this work, a custom integrated optical coherence tomography (OCT) imaging and optogenetic stimulation system was used to visualize and modulate the functioning D. melanogaster heart at the 3rd instar larval and early pupal developmental stages. The UAS/GAL4 dual genetic system was employed to express halorhodopsin (eNpHR2.0) and red-shifted channelrhodopsin (ReaChR), specifically in the fly heart. Details on preparing D. melanogaster for live OCT imaging and optogenetic pacing are provided. A lab-developed integration software processed the imaging data to create visual presentations and quantitative characteristics of Drosophila heart function. The results demonstrate the feasibility of initiating cardiac arrest and bradycardia caused by eNpHR2.0 activation and performing heart pacing upon ReaChR activation.

Section: Discussionmentioning

confidence: 99%

Developing <em>Drosophila melanogaster</em> Models for Imaging and Optogenetic Control of Cardiac Function

Gracheva

Matt

et al. 2022

JoVE

Self Cite

“…Segmentation of the endocardial lumen in OCT images was performed manually in this study, which is a commonly used approach and has been employed to produce the ground truths for developing automatic algorithms. 26,44,45 Recent advancements in automatic segmentation of the Drosophila cardiac lumen based on convolutional neural networks 44,45 could potentially help to reduce the time required for luminal area measurements in the early mouse heart. The measured axial resolution of OCT was lower than the theoretical value, which was likely caused by dispersion.…”

Section: Discussionmentioning

confidence: 99%

Live mechanistic assessment of localized cardiac pumping in mammalian tubular embryonic heart

Larina

2020

J. Biomed. Opt.

Significance: Understanding how the valveless embryonic heart pumps blood is essential to elucidate biomechanical cues regulating cardiogenesis, which is important for the advancement of congenital heart defects research. However, methods capable of embryonic cardiac pumping analysis remain limited, and assessing this highly dynamic process in mammalian embryos is challenging. New approaches are critically needed to address this hurdle. Aim: We report an imaging-based approach for functional assessment of localized pumping dynamics in the early tubular embryonic mouse heart. Approach: Four-dimensional optical coherence tomography was used to obtain structural and Doppler hemodynamic imaging of the beating heart in live mouse embryos at embryonic day 9.25. The pumping assessment was performed based on the volumetric blood flow rate, flow resistance within the heart tube, and pressure gradient induced by heart wall movements. The relation between the blood flow, the pressure gradient, and the resistance to flow were evaluated through temporal analyses and Granger causality test. Results: In the ventricles, our method revealed connections between the temporal profiles of pressure gradient and volumetric blood flow rate. Statistically significant causal relation from the pressure gradient to the blood flow was demonstrated. Our analysis also suggests that cardiac pumping in the early ventricles is a combination of suction and pushing. In contrast, in the outflow tract, where the conduction wave is slower than the blood flow, we did not find significant causal relation from pressure to flow, suggesting that, different from ventricular regions, the local active contraction of the outflow tract is unlikely to drive the flow in that region. Conclusions: We present an imaging-based approach that enables localized assessment of pumping dynamics in the mouse tubular embryonic heart. This method creates a new opportunity for functional analysis of the pumping mechanism underlying the developing mammalian heart at early stages and could be useful for studying biomechanical changes in mutant embryonic hearts that model congenital heart defects.

“…Innovative designs and implementations of OCT probes [ 86 , 87 ] can potentially inspire new strategies of integrating the OCT imaging head with the embryo culturing setup, which might lead to an improved experimental environment and condition for live mouse embryonic imaging. Image processing methods to extract specific features are increasingly demanded for the assessment of rich information provided by OCT, and to this end, deep-learning-enabled algorithms developed for OCT embryonic heart images [ 88 , 89 ] could have a profound impact on increasing the efficiency of analyzing the OCT cardiodynamic data. Microscopic particle image velocimetry (µPIV) is an important technique for the measurement of fluid flows; OCT-µPIV as an advanced high-resolution, depth-resolved PIV method has been demonstrated for dynamic flow imaging of chick embryos [ 90 ], which complements Doppler OCT by resolving the flow perpendicular to the OCT imaging beam, promising for robust quantification of hemodynamics in the mouse embryonic cardiovascular system.…”

Section: Perspective On Future Developmentsmentioning

confidence: 99%

Embryonic Mouse Cardiodynamic OCT Imaging

Lopez

2020

JCDD

The embryonic heart is an active and developing organ. Genetic studies in mouse models have generated great insight into normal heart development and congenital heart defects, and suggest mechanical forces such as heart contraction and blood flow to be implicated in cardiogenesis and disease. To explore this relationship and investigate the interplay between biomechanical forces and cardiac development, live dynamic cardiac imaging is essential. Cardiodynamic imaging with optical coherence tomography (OCT) is proving to be a unique approach to functional analysis of the embryonic mouse heart. Its compatibility with live culture systems, reagent-free contrast, cellular level resolution, and millimeter scale imaging depth make it capable of imaging the heart volumetrically and providing spatially resolved information on heart wall dynamics and blood flow. Here, we review the progress made in mouse embryonic cardiodynamic imaging with OCT, highlighting leaps in technology to overcome limitations in resolution and acquisition speed. We describe state-of-the-art functional OCT methods such as Doppler OCT and OCT angiography for blood flow imaging and quantification in the beating heart. As OCT is a continuously developing technology, we provide insight into the future developments of this area, toward the investigation of normal cardiogenesis and congenital heart defects.