A Markerless Pose Estimator Applicable to Limbless Animals

Abstract

The analysis of kinematics, locomotion, and spatial tasks relies on the accurate detection of animal positions and pose. Pose and position can be assessed with video analysis programs, the “trackers.” Most available trackers represent animals as single points in space (no pose information available) or use markers to build a skeletal representation of pose. Markers are either physical objects attached to the body (white balls, stickers, or paint) or they are defined in silico using recognizable body structures (e.g., joints, limbs, color patterns). Physical markers often cannot be used if the animals are small, lack prominent body structures on which the markers can be placed, or live in environments such as aquatic ones that might detach the marker. Here, we introduce a marker-free pose-estimator (LACE Limbless Animal traCkEr) that builds the pose of the animal de novo from its contour. LACE detects the contour of the animal and derives the body mid-line, building a pseudo-skeleton by defining vertices and edges. By applying LACE to analyse the pose of larval Drosophila melanogaster and adult zebrafish, we illustrate that LACE allows to quantify, for example, genetic alterations of peristaltic movements and gender-specific locomotion patterns that are associated with different body shapes. As illustrated by these examples, LACE provides a versatile method for assessing position, pose and movement patterns, even in animals without limbs.

A novel approach to quantifying inter-individual distance in insects

“…The recorded videos can subsequently be analysed by all commonly used tracking softwares (e.g. Lace [57]).…”

“…Flies were recorded at 50 fps using a Motion Traveller500 camera (IS, Imaging Solutions GmbH, Eningen, Germany) and TroubelPix video capturing software (NorPix Inc., Montreal, QC, Canada). Subsequently, videos were tracked using ivTrace (part of ivTools https://opensource.cit-ec.de/projects/ivtools by Dr. Jens P. Lindemann; Bielefeld University) and LACE [57] . Both trackers use image differences to track the centre of mass over the time course of the experiment, determining the flies position and orientation in a 2-dimensional space.…”

The caloric value of food intake structurally adjusts a neuronal mushroom body circuit mediating olfactory learning inDrosophila

“…Data capture was executed using TroublePix software from NorPix Inc., and facilitated through a MotionTraveller 500 camera (Imaging Solutions GmbH). Each fruit fly's trajectory, consisting of position and orientation in each camera frame, was meticulously tracked using LACE, an automatic animal tracking system ( Garg et al 2022 ). Locomotion speed was determined by calculating the difference vector between the centers of mass in two consecutive frames.…”

Axon demyelination and degeneration in a zebrafishspastizinmodel of hereditary spastic paraplegia

“…Zebrafish locomotion was tracked with Limbless Animal traCkEr (LACE), a MATLAB R2012b script (The MathWorks Inc., Natick, Massachusetts, USA) (Garg et al, 2022).…”