A Run-Length Encoding Approach for Path Analysis ofC. elegansSearch Behavior

Li Huang,Jacob Furst,Hongkyun Kim,Daniela Raicu

doi:10.1155/2016/3516089

Abstract

The nematode Caenorhabditis elegans explores the environment using a combination of different movement patterns, which include straight movement, reversal, and turns. We propose to quantify C. elegans movement behavior using a computer vision approach based on run-length encoding of step-length data. In this approach, the path of C. elegans is encoded as a string of characters, where each character represents a path segment of a specific type of movement. With these encoded string data, we perform k-means cluster analysis to distinguish movement behaviors resulting from different genotypes and food availability. We found that shallow and sharp turns are the most critical factors in distinguishing the differences among the movement behaviors. To validate our approach, we examined the movement behavior of tph-1 mutants that lack an enzyme responsible for serotonin biosynthesis. A k-means cluster analysis with the path string-encoded data showed that tph-1 movement behavior on food is similar to that of wild-type animals off food. We suggest that this run-length encoding approach is applicable to trajectory data in animal or human mobility data.

Highlights

C. elegans is an important genetic model organism relevant to human biology and disease, as its genome is surprisingly similar to that of humans (40% homologous) [1]
Genes encoding tryptophan hydroxylase, which is the key enzyme for serotonin biosynthesis, are conserved in human and C. elegans [2]
We propose to encode the path using run-length encoding, which is a data compression algorithm for sequences of data developed by Duda et al [17] and extract a set of features that will quantify the characteristics of the path

Summary

Introduction

C. elegans is an important genetic model organism relevant to human biology and disease, as its genome is surprisingly similar to that of humans (40% homologous) [1]. By comparing the locomotory behaviors of C. elegans wild-type and tph-1 animals under two different conditions (in the presence and absence of food), we expect to gain insights into understanding how certain genes influence human emotional and congenital disorders. Video data recorded with the trackers can be further analyzed by quantifying the differences in the worm body and movement characteristics The differences in these characteristics allow comparing food search behavior across different types of worms and understanding what genetic mutation produces a certain defect in the worm movement. We (1) quantify the path of a worm as a string of symbols where each symbol represents a segment of a certain type of movement (shallow or sharp turn) and (2) learn the similarities and differences in C. elegans locomotory behaviors by comparing their string-encoded path data

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Conclusion