Arena Worm Tracker
C. elegans in a microfluidic behavior arena, captured with a single worm tracker.
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 file:
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. Please note that no AutoCAD (.dwg) version is currently available due to curve complexity. However, most print shops can produce photomasks from .eps formats.
MATLAB Tracking and Analysis scripts:
MATLAB scripts (m-files) accomplish the following basic tasks:
- ArenaTracker: Segment video file (.AVI) 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.
Contact:
dalbrecht@rockefeller.edu