Worm Analysis System

Revision as of 17:55, 16 February 2010

There is a compelling need for improved software systems for delineating the C.elegans worms in time-lapse image sequences and tracking their movements. Segmentation and tracking provide the basis for making quantitative measurements of worm morphology, and various aspects of their dynamic behaviors. To facilitate the quantitative studies of worm behaviors, we developed a automated worm analysis system which is open-source and could be adopted by all researchers in the c.elegans community.

News

• 2010-02-14: Wiki Page for Worm Analysis System Created.

System Overview

Figure 1: Main Window of the System

Figure1 shows a screenshot of the main window of the system.

• Menu: the menu provides operations like file operations and editing operations which allow user to edit (reverse, delete and correct)selected worms in the tracking window.
• Toolbar: the toolbr provides three buttons (figure2: pause tracking, start/resume tracking, start tracking from a saved point) for controlling the tracking process. Users can pause tracking at any timepoint and do some observation or interactive editing when necessary. The thrid button make it possible for the user to start tracking from any saved tracking result which stores worm shapes, features and identities. Thus the user don't need to start over the tracking if the program was closed normally or abnormally.

Figure 2: Toolbar

• Input and Output: the input and output section allows users to specify the directory of image sequence and the directory for storing tracking result. For each frame, the tracking result of it includes a txt file storing the worm structure(centerline and contour points), a excel file storing extracted features(motion state, shape and motion features, events, etc.) and a png image saved from the tracking window. The results could be explored at anytime during or after the tracking Explore Results.
• Settings: the settings section allows users to specify settings for core processing algorithms. Please refer to Settings for detailed information about these settings.
• Tracking Window: the tracking window includes the "tracking view" and "foreground view". The tracking view displays the centerline and contour of tracked worms, and also their identity and motion states(F=Forward, R=Reversal, P=Pausing, O=Omega Bend, C=Physical Contact). The foreground view shows the label image for foreground objects obtained by background subtraction method, it could help the user choose the right binarization parameters.
• Log Window: the log window displays the log of the tracking process. More detailed information about the tracking process is displayed in another terminal window.

Overview

System Features

Multiple Linked Views

Edit

Settings

Keyboard Shortcuts

Explore Results

If the directory for saving tracking results is provided, users could explore the result after tracking, or during the tracking process simply by pausing the tracking first, checking the "explore result" box and sliding the "frame number" slider.

Contributors to the New Worm System:

• Yu Wang
• Isaac Abbott

For information of our old worm project, please refer to [Old Worm Project]. ==

References

• [1] Yu Wang, Roysam Badrinath, “Joint Tracking and Locomotion State Recognition of C.elegans from Time-Lapse Image Sequences,” IEEE International Symposium on Biomedical Imaging (ISBI) 2010 (oral presentation).
• [2] Roussel Nicolas, Morton Christine A, Finger Fern P, Roysam Badrinath, “A computational model for C. elegans locomotory behavior : Application to multiworm tracking,” IEEE transactions on biomedical engineering, pp. 1786-1797, 2007.
• [3] Katsunori Hoshi, Ryuzo Shingai, “Computer-driven automatic identification of locomotion states in Caenorhabditis elegans,” J Neurosci Methods, vol. 157(2), pp.355-363, 2006.
• [4] Huang KM, Cosman P, Schafer WR, “Machine vision based detection of omega bends and reversals in C. elegans,” Journal of Neuroscience Methods, vol. 158, Issue 2, pp. 323-336, 2006.
• [5] Nicolas Roussel, "A Computational Model for C.elegans locomotory behavior: Application to Multi-Worm tracking", Phd Thesis, 2007.
• [6] 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) 2007, pp. 1240-1243, 2007.
• [7] Fontaine, E., Barr, A., Burdick, J. W., “Model-based tracking of multiple worms and fish,” ICCV Workshop on Dynamical Vision, 2007.
• [8] Fontaine, E., Barr, A., Burdick, J. W., "Model-based tracking of multiple worms and fish", In ICCV Workshop on Dynamical Vision, 2007.
• [9] Wei Geng; Cosman, P.; Berry, C.C.; Zhaoyang Feng; Schafer, W.R., “Automatic tracking, feature extraction and classification of C. elegans phenotypes,” Biomedical Engineering, IEEE Transactions on, vol.51, no.10, pp.1811-1820, 2004.
• [10] Isard, M.; Blake, A., “A mixed-state condensation tracker with automatic model-switching,” Computer Vision, 1998. Sixth International Conference on, pp.107-112,1998.
• [11] G.J. Stephens et al., "Dimensionality and Dynamics in the Behavior of C. elegans", PLoS Comp. Biol., 2008.