Compilation of information and code bases related to open-source trackers for C. elegans
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README.md

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 Build Status no
Python Michael Currie Feature-complete, beta Build Status PyPI package
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