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