C. elegans web site for Pamela Cosman

Publications

  1. J. Baek, P. Cosman, Z. Feng, J. Silver, and W.R. Schafer, "Using machine vision to analyze and classify C. elegans behavioral phenotypes quantitatively," Journal of Neuroscience Methods, Vol. 118, pp. 9-21, 2002. PDF

  2. W. Geng, P. Cosman, J.-H. Baek, C. Berry, W.R. Schafer, "Quantitative Classification and Natural Clustering of C. elegans Behavioral Phenotypes," Genetics. Vol. 165, pp. 1117--1126, November 2003. PDF

  3. W. Geng, P. Cosman, Z. Feng, C. Berry, W.R. Schafer, "Automatic Tracking, Feature Extraction and Classification of C. elegans Phenotypes," IEEE Transactions on Biomedical Engineering, Vol. 51, No. 10, pp. 1811--1820, October 2004. PDF

  4. W. Geng, P.C. Cosman, M. Palm, W. Schafer, "C. elegans Egg-Laying Detection and Behavior Study using Image Analysis," Eurasip Journal on Applied Signal Processing, Special issue on Advances in Intelligent Vision Systems: Methods and Applications-- Part II, vol 2005, no. 14, pp. 2229-2240, August 2005. PDF

  5. K.M. Huang, P.C. Cosman, and W. Schafer, "Machine Vision Based Detection of Omega Bends and Reversals in C. elegans," Journal of Neuroscience Methods, Vol. 158, Issue 2, pp. 323-336, December 2006.

  6. K.M. Huang, P.C. Cosman, and W. Schafer, "Automated Detection and Analysis of Foraging Behavior in C. elegans," accepted by Journal of Neuroscience Methods.

  7. K.M. Huang, P.C. Cosman, and W. Schafer, "Using Articulated Models for Tracking Multiple C. elegans in Physical Contact," accepted by Journal of Signal Processing Systems. PDF

  8. W. Geng, P. Cosman, J.-H. Baek, C. Berry and W.R. Schafer, "Image Feature Extraction and Natural Clustering of Worm Body Shapes and Motion Characteristics" IASTED International Conference on Signal and Image Processing (SIP 2003), August 13-15, 2003, Honolulu, Hawaii. PDF

  9. W. Geng, P. Cosman, C. Huang, and W.R. Schafer, "Automated Worm Tracking and Classification" Proceedings 37th Asilomar Conference on Signals, Systems and Computers, pages 2063-2068, Nov 9-12, 2003, Pacific Grove, California. PDF

  10. W. Geng, P. Cosman, and W. Schafer, "Detecting attached worm eggs using deformable template matching," Proceedings IASTED International Conference on Computers, Graphics and Imaging (CGIM 2004), August 16-18, 2004, Kauai, Hawaii, pp. 309-314.

  11. K.M. Huang, P.C. Cosman, and W. Schafer, "Automated tracking of multiple C. elegans with articulated models," IEEE International Symposium on Biomedical Imaging (ISBI'07), pp. 1240-1243. PDF

  12. K.M. Huang, P.C. Cosman, and W. Schafer, "Automated Detection and Analysis of Foraging Behavior in C. elegans," 2008 IEEE Southwest Symposium on Image Analysis and Interpretation (SSIAI 2008), March 24-26, 2008, Santa Fe, New Mexico, USA.

Multi-worm Tracking: Videos and Software

Our multi-worm tracking experiments are described in brief preliminary form in a conference paper(K.M. Huang, P.C. Cosman, and W. Schafer, ``Automated tracking of multiple C. elegans with articulated models,'' IEEE International Symposium on Biomedical Imaging (ISBI'07), pp. 1240-1243. PDF) and have also been submitted as a full-length journal paper. This web site contains the 29 worms videos in avi format, and associated software in Matlab, which were used in these papers.

In each video, two worms were tracked and their body poses were simulated in each frame. Note that in 26 of the videos, the worms were identified correctly after they touched each other, but in three videos (npr1, npr13, and npr28), the worms were identified incorrectly after they touch each other. Incorrect identification means that worm 1 from before the touching was identified as worm 2 afterwards, and worm 2 from before the touching was identified as worm 1 afterwards.

The 29 videos are:

Here is a zip file with all the videos.

All source code used in these experiments is available from this web site. The main program is the file named “ucsdTrackNew.m”. The user should first extract image frames (in jpeg format) from the input videos and modify the path of images in the script appropriately. The Microsoft mpeg4v2 codec should be installed in the computer in advance.

The Matlab files contained in the zip file are the following:

appendSegs.m myImRead.m showsegImAll.m backrem.m pt2seg.m showsegIm.m compareBodyPts.m relAllPos.m showWormBodyPts.m compareBodyPtsnew.m run.m sq_distance_ft.m ComputeAngleCh.m sampleWithR.m subSegs.m curv_diff.m sampleWormBodyPts.m Track.m drawWorms.m scoreAllPts.m ucsdTrack.m findCandidateLinks.m scoreBodyPts.m ucsdTrackNew1.m flip.m showModelPtsW.m ucsdTrackNew.m

Here is a zip file with all the matlab source files.