The Schafer Lab, at the MRC Laboratory of Molecular Biology, Cambridge, UK, developed the Worm Analysis Toolbox to work with data from the Worm Tracker 2.0 (WT2). The open-worm-analysis-toolbox package is a port of the last version of the Worm Analysis Toolbox, version 1.3.4.
Dr. Eviatar "Ev" Yemini, for all the original Matlab code built as part of the WormBehavior database, written as part of his doctorate at the Schafer Lab. Without him this project would not have been possible. His PhD thesis was partly based on his work creating the analysis package we ported to form the basis of the package.
Dr. Tadas Jucikas, post-doctoral scholar at the Schafer Lab, for co-authoring the Worm Tracker 2.0 analysis package with Ev.
Dr. William "Bill" Schafer, Schafer Lab eponym, for allowing us to use and adapt Ev's code.
Dr. André Brown, formerly a post-doctoral scholar at the Schafer Lab, and now principal investigator at the Brown Lab at Imperial College London, for contributions to the original Matlab code and for his work on behavioural motifs, which we hope to add. With Dr. Kerr he created the tracker-commons format.
Dr. Rex Kerr, principal investigator at the Kerr Lab at Janelia Research Campus, for his work on the tracker-commons format.
Barry Bentley, PhD student at the Schafer Lab, for his ongoing support of our use of their code.
Laura Grundy, lab assistant at the Schafer Lab, for filming many hundreds of hours of C. elegans videos.
- WT2 employs Java (version 1.6) for the tracking software and Matlab (version 2010a) for the analysis software. Standard Matlab functions are used along with the Image Processing, Statistics, and Bioinformatics toolboxes.
- Special thanks and acknowledgements are due to Christopher J. Cronin and Paul W. Sternberg at Caltech's Sternberg Lab for supplying the Matlab code from their publication, "An automated system for measuring parameters of nematode sinusoidal movement" (Cronin et al. 2005), for use in the locomotion features.
- Joan Lasenby and Nick Kingsbury were an invaluable resource for computer vision questions.
- Andrew Deonarine, Richard Samworth, Sreenivas Chavali, Guilhem Chalancon, Sarah Teichmann, and Dr. M. Madan Babu provided a wealth of help and information for the bioinformatic clustering and statistics.
- Thanks to the OpenCV computer vision library.
- Thanks to Gerald Dalley for the videoIO toolbox for Matlab.
Thanks and acknowledgements are due for the following freely available code:
- export_fig function by Oliver Woodford
- notBoxPlot function by Rob Campbell
- swtest function by Ahmed Ben Saïda
- fexact function by Michael Boedigheimer
- rdir function by Gus Brown
- xlswrite1 function by Matt Swartz
Dr. Stephen Larson, OpenWorm's project coordinator, for the original idea to adapt Ev's code and for encouragement and support.
- Dr. James "Jim" Hokanson for improving upon the original Matlab code, doing much of the translation of the code into this Python repository, overall architectural decisions, documentation, and for his Matlab Standard Library.
- Dr. Chee Wai Lee for his work on this repository and tracker-commons.
- Michael Currie for helping with the translation into Python, and helping with repository documentation.
- Dr. Avelino Javer
- Dr. Rex Kerr
Past team members:
- Aidan Rocke who worked on porting Dr. Brown's behavioural syntax code into Python.
- Chris Linzy
- Chris Barnes
- Joe Bowen