Tracker Commons

The Tracker Commons is a repository of documentation, software, and discussions that enable labs to share their worm tracking data and analysis routines.

The WCON format

The Worm tracker Commons Object Notation (WCON) file format provides a simple way to share C. elegans tracking data between labs and analysis packages.

WCON uses the widely-supported JSON file format, so almost any language can easily import the data. WCON specifies a few entries that you should include in a JSON "Object" (a.k.a. a map or dictionary) that will let readers easily extract basic information about worms.

Here's an example!

{
    "metadata":{
        "who":"Open Worm",
        "timestamp":"2016-01-22T17:44:48",
        "protocol":"Numbers made up by hand for an example!"
    },
    "units":{"t":"s", "x":"mm", "y":"mm"},
    "data":[
        {"id":"worm1", "t":[0.1], "x":[[0.33, 0.65, 0.8, 1.1, 1.2]], "y":[[2.31, 2.25, 2.0, 1.87, 1.66]]},
        {"id":"worm1", "t":[0.3], "x":[[0.27, 0.6, 0.75, 1.0, 1.1]], "y":[[2.4, 2.3, 2.07, 1.78, 1.75]]}
    ]
}

This file contains data for a single worm over two timepoints. The worm's body is represented as five points along the worm's spine.

Tracker Commons software for reading and writing WCON files

The Tracker Commons repository contains implementations for reading and writing WCON data for a variety of languages. Browse the src directory to learn more!

Language	Principal Author	Capabilities	Test Status	Packaged?
Scala	Rex Kerr	Feature-complete, beta		no
Python	Michael Currie	Feature-complete, beta
Java	Rex Kerr	Feature-complete, beta	none	no
Matlab	Jim Hokanson	Runnable implementation (alpha)	n/a	no
R	Rex Kerr	Lightweight wrapper using rscala (alpha)	none	no
Julia	Rex Kerr	Runnable implementation (alpha)	none	no
Octave	Chee Wai Lee	Lightweight wrapper to Python version	none	no
Rust	n/a	Preliminary notes only	n/a	no