Mapping the spatiotemporal dynamics of calcium signaling in cellular neural networks using optical flow

An optical flow gradient algorithm was applied to spontaneously forming net- works of neurons and glia in culture imaged by fluorescence optical microscopy in order to map functional calcium signaling with single pixel resolution. Optical flow estimates the direction and speed of motion of objects in an image between subsequent frames in a recorded digital sequence of images (i.e. a movie). Computed vector field outputs by the algorithm were able to track the spatiotemporal dynamics of calcium signaling pat- terns. We begin by briefly reviewing the mathematics of the optical flow algorithm, and then describe how to solve for the displacement vectors and how to measure their reliability. We then compare computed flow vectors with manually estimated vectors for the progression of a calcium signal recorded from representative astrocyte cultures. Finally, we applied the algorithm to preparations of primary astrocytes and hippocampal neurons and to the rMC-1 Muller glial cell line in order to illustrate the capability of the algorithm for capturing different types of spatiotemporal calcium activity. We discuss the imaging requirements, parameter selection and threshold selection for reliable measurements, and offer perspectives on uses of the vector data.Comment: 23 pages, 5 figures. Peer reviewed accepted version in press in Annals of Biomedical Engineerin

A particle filter to reconstruct a free-surface flow from a depth camera

We investigate the combined use of a Kinect depth sensor and of a stochastic data assimilation method to recover free-surface flows. More specifically, we use a Weighted ensemble Kalman filter method to reconstruct the complete state of free-surface flows from a sequence of depth images only. This particle filter accounts for model and observations errors. This data assimilation scheme is enhanced with the use of two observations instead of one classically. We evaluate the developed approach on two numerical test cases: a collapse of a water column as a toy-example and a flow in an suddenly expanding flume as a more realistic flow. The robustness of the method to depth data errors and also to initial and inflow conditions is considered. We illustrate the interest of using two observations instead of one observation into the correction step, especially for unknown inflow boundary conditions. Then, the performance of the Kinect sensor to capture temporal sequences of depth observations is investigated. Finally, the efficiency of the algorithm is qualified for a wave in a real rectangular flat bottom tank. It is shown that for basic initial conditions, the particle filter rapidly and remarkably reconstructs velocity and height of the free surface flow based on noisy measurements of the elevation alone

Transport-Based Neural Style Transfer for Smoke Simulations

Artistically controlling fluids has always been a challenging task. Optimization techniques rely on approximating simulation states towards target velocity or density field configurations, which are often handcrafted by artists to indirectly control smoke dynamics. Patch synthesis techniques transfer image textures or simulation features to a target flow field. However, these are either limited to adding structural patterns or augmenting coarse flows with turbulent structures, and hence cannot capture the full spectrum of different styles and semantically complex structures. In this paper, we propose the first Transport-based Neural Style Transfer (TNST) algorithm for volumetric smoke data. Our method is able to transfer features from natural images to smoke simulations, enabling general content-aware manipulations ranging from simple patterns to intricate motifs. The proposed algorithm is physically inspired, since it computes the density transport from a source input smoke to a desired target configuration. Our transport-based approach allows direct control over the divergence of the stylization velocity field by optimizing incompressible and irrotational potentials that transport smoke towards stylization. Temporal consistency is ensured by transporting and aligning subsequent stylized velocities, and 3D reconstructions are computed by seamlessly merging stylizations from different camera viewpoints.Comment: ACM Transaction on Graphics (SIGGRAPH ASIA 2019), additional materials: http://www.byungsoo.me/project/neural-flow-styl

Uncovering wall-shear stress dynamics from neural-network enhanced fluid flow measurements

Friction drag from a turbulent fluid moving past or inside an object plays a crucial role in domains as diverse as transportation, public utility infrastructure, energy technology, and human health. As a direct measure of the shear-induced friction forces, an accurate prediction of the wall-shear stress can contribute to sustainability, conservation of resources, and carbon neutrality in civil aviation as well as enhanced medical treatment of vascular diseases and cancer. Despite such importance for our modern society, we still lack adequate experimental methods to capture the instantaneous wall-shear stress dynamics. In this contribution, we present a holistic approach that derives velocity and wall-shear stress fields with impressive spatial and temporal resolution from flow measurements using a deep optical flow estimator with physical knowledge. The validity and physical correctness of the derived flow quantities is demonstrated with synthetic and real-world experimental data covering a range of relevant fluid flows

Some comments on particle image displacement velocimetry

Laser speckle velocimetry (LSV) or particle image displacement velocimetry, is introduced. This technique provides the simultaneous visualization of the two-dimensional streamline pattern in unsteady flows as well as the quantification of the velocity field over an entire plane. The advantage of this technique is that the velocity field can be measured over an entire plane of the flow field simultaneously, with accuracy and spatial resolution. From this the instantaneous vorticity field can be easily obtained. This constitutes a great asset for the study of a variety of flows that evolve stochastically in both space and time. The basic concept of LSV; methods of data acquisition and reduction, examples of its use, and parameters that affect its utilization are described