Introduction

Overview

We developed a microfluidics-based system for the analysis of C. elegans locomotory behavior in response to defined spatial and temporal stimulus patterns. We designed 2 x 2 cm structured arenas with regulated fluid flow that allow C. elegans to perform crawling-like locomotion resembling normal behavior on agar surfaces. Stimuli are delivered in the fluid phase and odor-evoked behaviors in the arena are automatically captured, segmented and analyzed using the MATLAB scripts available here.

Publication

Albrecht, D.R. & Bargmann, C.I. High-content behavioral analysis of Caenorhabditis elegans in precise spatiotemporal chemical environments. Nature Methods (2011), doi:10.1038/nmeth.1630

Photomask Design

A photomask file suitable for fabricating 22 mm arenas presenting chemical pulses, stripes, and gradients is available in Postscript (.eps) format. This file replaces Supplementary File 1 in the publication, which was slightly altered upon conversion.

MATLAB Tracking and Analysis scripts:

MATLAB scripts (m-files) accomplish the following basic tasks:

• ArenaTracker: Segments video file to obtain worm tracks. Code adapted from the parallel worm tracker.
• SegmentTracks: Identifies instantaneous behavioral states from worm tracks and morphological data.
• Ethogram: Displays ethogram and summarizes behavioral state probability and speed over time.
• WormDensity: Summarizes behavioral state and speed data over space and time.

Video tracking, behavior segmentation, and data analysis were performed using MATLAB R2016+ with the Image Processing toolbox. Scripts have been tested on Windows 10.

Locomotion in Microfluidic Arenas

C. elegans in a microfluidic behavior arena, captured with a single worm tracker.