Hello and welcome to Track-A-Worm, the advanced C. elegans tracking system for Matlab.
Track-A-Worm is an automated single-worm tracker designed for recording and
quantifying detailed bending and locomotory behavior of C. elegans.
Here's what you need:
Here's what we use in the lab:
The software includes seven modules: Calibrate, Record, Playback, Batch Spline,
Fit Spline, Analyze, and Batch Analyze.
Track-A-Worm converts gray images into binary images followed by automatic head
identification and placement of 13 markers along a deduced spline. It can extract
and quantify a variety of parameters, including distance traveled, average speed,
distance/time/speed of forward and backward locomotion, frequency and amplitude of
dominant bends, overall bending activities measured as root mean square, and sum
of all bends. It also plots worm travel path, bend trace, and bend frequency spectrum.
All functionality is performed through graphical user interfaces.
- Windows 7 or 8 PC, 32 or 64-bit supported
- Matlab with the following toolboxes:
- Image Acquisition Toolbox
- Image Processing Toolbox
- Instrument Control Toolbox
- Signal Processing Toolbox
- Digital camera with Matlab support through WinVideo, DCAM, etc.
- X-Y stage with computer control capability
- National Instruments MyDAQ (optional - for optogenetic experiments)
|Track-A-Worm's algorithm detects the head and tail of the worm. It then places 13
equally-spaced markers along the worm body to form a spline.
|Recording module: This module connects to the camera, stage, and
DAQ (if applicable - for optogenetic experiments) in order to track the worm as it moves across the
Petri dish. Output is a numerical series of bitmap files, as well as a support
file which records the movement of the stage. These data are analyzed to
produce a full dataset comprising every position of the worm spline (in micrometers)
|Optogenetic stimulation: This sub-module of the Recording module allows
the user to control TTL lasers via the National Instruments MyDAQ.
The user can define timing routines for up to three lasers, or can manually control all three
simultaneously using an on/off button.
|Playback module: This module allows the user to preview and
manipulate the recording. Functions include previewing the thresholded image (useful when fitting
splines), cutting frames, reducing frame rate, and exporting a movie. Movies can be exported with
spline overlays, if available.
|Spline fitting: This module analyzes each image and produces
a spline which is made up of 13 points equally spaced along the worm body. Images are
previewed 10 frames at a time through this interface, and there are manual controls
which allow re-fitting and manipulation of the automatically-generated splines if the fitting
algorithm makes an error.
|Curve Analyzer: This module produces best-fit
circles to each worm bend, expressed as a percentage of circle radius compared to overall worm length. Curves are delineated
by the inflection points of the worm. Also note that if the user designates a ventral/dorsal direction
during the recording process, the curve data will reflect this information. Solid lines denote ventral curves,
while dotted lines denote dorsal curves.
|Analysis module: This module contains the analysis tools of Track-A-Worm.
Relevant tools include the ability to describe worm bending behaviors such as maximum excursion,
root-mean-square, sum of all bends, and dominant bending frequency, as well as movement behaviors
such as amplitude, speed, distance, and the percentage of time spent in forwards/backwards motion.
The bend trace and worm path (centroid or any point)
can be displayed. All results can be exported using this module. Note that curve analysis is
not included in this function because it requires an additional degree of user
interaction which warrants its own module.
Track-A-Worm is written by me, S. Jason Wang, MD. Please do not hesitate to
contact me with questions or comments. I am currently a medical resident so I have limited time to update the software,
but will provide you with help to the best of my abilities.