https://github.com/openworm/tracker-commons
Compilation of information and code bases related to open-source trackers for C. elegans
https://github.com/openworm/tracker-commons
Last synced: about 1 year ago
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Compilation of information and code bases related to open-source trackers for C. elegans
- Host: GitHub
- URL: https://github.com/openworm/tracker-commons
- Owner: openworm
- Created: 2015-07-07T01:58:37.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2025-03-20T16:07:47.000Z (over 1 year ago)
- Last Synced: 2025-03-20T16:40:53.875Z (over 1 year ago)
- Language: Scala
- Homepage:
- Size: 847 KB
- Stars: 12
- Watchers: 17
- Forks: 12
- Open Issues: 29
-
Metadata Files:
- Readme: README.md
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README
# 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](http://json.org) 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!
```JSON
{
"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](src/scala) | Rex Kerr | Feature-complete, beta | [](https://semaphoreci.com/ichoran/tracker-commons) | no |
| [Python](src/Python) | Michael Currie | Feature-complete, beta | [](https://travis-ci.org/openworm/tracker-commons) | [](http://badge.fury.io/py/wcon) |
| [Java](src/java) | Rex Kerr | Feature-complete, beta | none | no |
| [Matlab](src/Matlab) | Jim Hokanson | Runnable implementation (alpha) | n/a | no |
| [R](src/R) | Rex Kerr | Lightweight wrapper using rscala (alpha) | none | no |
| [Julia](src/julia) | Rex Kerr | Runnable implementation (alpha) | none | no |
| [Octave](src/octave) | Chee Wai Lee | Lightweight wrapper to Python version | none | no |
| [Rust](src/Rust) | n/a | Preliminary notes only | n/a | no |