High accuracy decoding of dynamical motion from a large retinal population

Motion tracking is a challenge the visual system has to solve by reading out the retinal population. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar position can be reconstructed from retinal activity with a precision in the hyperacuity regime using a linear decoder acting on 100+ cells. The classical view would have suggested that the firing rates of the cells form a moving hill of activity tracking the bar's position. Instead, we found that ganglion cells fired sparsely over an area much larger than predicted by their receptive fields, so that the neural image did not track the bar. This highly redundant organization allows for diverse collections of ganglion cells to represent high-accuracy motion information in a form easily read out by downstream neural circuits.Comment: 23 pages, 7 figure

Scalable Estimation of Precision Maps in a MapReduce Framework

This paper presents a large-scale strip adjustment method for LiDAR mobile mapping data, yielding highly precise maps. It uses several concepts to achieve scalability. First, an efficient graph-based pre-segmentation is used, which directly operates on LiDAR scan strip data, rather than on point clouds. Second, observation equations are obtained from a dense matching, which is formulated in terms of an estimation of a latent map. As a result of this formulation, the number of observation equations is not quadratic, but rather linear in the number of scan strips. Third, the dynamic Bayes network, which results from all observation and condition equations, is partitioned into two sub-networks. Consequently, the estimation matrices for all position and orientation corrections are linear instead of quadratic in the number of unknowns and can be solved very efficiently using an alternating least squares approach. It is shown how this approach can be mapped to a standard key/value MapReduce implementation, where each of the processing nodes operates independently on small chunks of data, leading to essentially linear scalability. Results are demonstrated for a dataset of one billion measured LiDAR points and 278,000 unknowns, leading to maps with a precision of a few millimeters.Comment: ACM SIGSPATIAL'16, October 31-November 03, 2016, Burlingame, CA, US

Optical Flow on Evolving Surfaces with an Application to the Analysis of 4D Microscopy Data

We extend the concept of optical flow to a dynamic non-Euclidean setting. Optical flow is traditionally computed from a sequence of flat images. It is the purpose of this paper to introduce variational motion estimation for images that are defined on an evolving surface. Volumetric microscopy images depicting a live zebrafish embryo serve as both biological motivation and test data.Comment: The final publication is available at link.springer.co

Learning Ground Traversability from Simulations

Mobile ground robots operating on unstructured terrain must predict which areas of the environment they are able to pass in order to plan feasible paths. We address traversability estimation as a heightmap classification problem: we build a convolutional neural network that, given an image representing the heightmap of a terrain patch, predicts whether the robot will be able to traverse such patch from left to right. The classifier is trained for a specific robot model (wheeled, tracked, legged, snake-like) using simulation data on procedurally generated training terrains; the trained classifier can be applied to unseen large heightmaps to yield oriented traversability maps, and then plan traversable paths. We extensively evaluate the approach in simulation on six real-world elevation datasets, and run a real-robot validation in one indoor and one outdoor environment.Comment: Webpage: http://romarcg.xyz/traversability_estimation

Global parameter identification of stochastic reaction networks from single trajectories

We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from live-cell fluorescence microscopy in image-based systems biology. In addition, fluctuation time-courses from, e.g., fluorescence correlation spectroscopy provide additional information about the system dynamics that can be used to more robustly infer parameters than when considering only mean concentrations. Estimating model parameters from a single experimental trajectory enables single-cell measurements and quantification of cell--cell variability. We propose a novel combination of an adaptive Monte Carlo sampler, called Gaussian Adaptation, and efficient exact stochastic simulation algorithms that allows parameter identification from single stochastic trajectories. We benchmark the proposed method on a linear and a non-linear reaction network at steady state and during transient phases. In addition, we demonstrate that the present method also provides an ellipsoidal volume estimate of the viable part of parameter space and is able to estimate the physical volume of the compartment in which the observed reactions take place.Comment: Article in print as a book chapter in Springer's "Advances in Systems Biology

Particle-filtering approaches for nonlinear Bayesian decoding of neuronal spike trains

The number of neurons that can be simultaneously recorded doubles every seven years. This ever increasing number of recorded neurons opens up the possibility to address new questions and extract higher dimensional stimuli from the recordings. Modeling neural spike trains as point processes, this task of extracting dynamical signals from spike trains is commonly set in the context of nonlinear filtering theory. Particle filter methods relying on importance weights are generic algorithms that solve the filtering task numerically, but exhibit a serious drawback when the problem dimensionality is high: they are known to suffer from the 'curse of dimensionality' (COD), i.e. the number of particles required for a certain performance scales exponentially with the observable dimensions. Here, we first briefly review the theory on filtering with point process observations in continuous time. Based on this theory, we investigate both analytically and numerically the reason for the COD of weighted particle filtering approaches: Similarly to particle filtering with continuous-time observations, the COD with point-process observations is due to the decay of effective number of particles, an effect that is stronger when the number of observable dimensions increases. Given the success of unweighted particle filtering approaches in overcoming the COD for continuous- time observations, we introduce an unweighted particle filter for point-process observations, the spike-based Neural Particle Filter (sNPF), and show that it exhibits a similar favorable scaling as the number of dimensions grows. Further, we derive rules for the parameters of the sNPF from a maximum likelihood approach learning. We finally employ a simple decoding task to illustrate the capabilities of the sNPF and to highlight one possible future application of our inference and learning algorithm