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LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals

Marco Pietro Abrate, Pascal Fua, Adám Gosztolai, Semih Günel, Victor Lobato Rios, Daniel Eduardo Morales Garza, Pavan P Ramdya, Helge Jochen Rhodin

LiftPose3D infers three-dimensional poses from two-dimensional data or from limited three-dimensional data. The approach is illustrated for videos of behaving Drosophila, mice, rats and macaques. Markerless three-dimensional (3D) pose estimation has become an indispensable tool for kinematic studies of laboratory animals. Most current methods recover 3D poses by multi-view triangulation of deep network-based two-dimensional (2D) pose estimates. However, triangulation requires multiple synchronized cameras and elaborate calibration protocols that hinder its widespread adoption in laboratory studies. Here we describe LiftPose3D, a deep network-based method that overcomes these barriers by reconstructing 3D poses from a single 2D camera view. We illustrate LiftPose3D's versatility by applying it to multiple experimental systems using flies, mice, rats and macaques, and in circumstances where 3D triangulation is impractical or impossible. Our framework achieves accurate lifting for stereotypical and nonstereotypical behaviors from different camera angles. Thus, LiftPose3D permits high-quality 3D pose estimation in the absence of complex camera arrays and tedious calibration procedures and despite occluded body parts in freely behaving animals.

NATURE PORTFOLIO2021

Cellular memory enhances bacterial chemotactic navigation in rugged environments

Adám Gosztolai

The response of microbes to external signals is mediated by biochemical networks with intrinsic time scales. These time scales give rise to a memory that impacts cellular behaviour. Here we study theoretically the role of cellular memory in Escherichia coli chemotaxis. Using an agent-based model, we show that cells with memory navigating rugged chemoattractant landscapes can enhance their drift speed by extracting information from environmental correlations. Maximal advantage is achieved when the memory is comparable to the time scale of fluctuations as perceived during swimming. We derive an analytical approximation for the drift velocity in rugged landscapes that explains the enhanced velocity, and recovers standard Keller-Segel gradient-sensing results in the limits when memory and fluctuation time scales are well separated. Our numerics also show that cellular memory can induce bet-hedging at the population level resulting in long-lived, multi-modal distributions in heterogeneous landscapes. Microbes respond to biochemical signals from the environment, a process known as chemotaxis. Using mathematical models, the authors explore the role of cellular memory in cell motion and show that, when swimming across a rugged chemoattractant landscape, E. coli extract spatio-temporal information to improve their navigation.

NATURE PUBLISHING GROUP2020