Inexpensive, Easy-To-Use, and Feature-Rich Worm Tracking.
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Transcript of Inexpensive, Easy-To-Use, and Feature-Rich Worm Tracking.
The Benefits
• Inexpensive
• Easy-to-Use
• Feature Rich
• A simple pipeline to Analysis
• Well-Documented (easily extended, updated, and maintained)
Inexpensive
• Works FAST and beautifully with CHEAP (<$30) USB cameras.
• Supports most stages:– Ludl & Prior now– National Instruments/Parker later
• Works well with any computer:– Windows, Mac, & Unix variants
• Does NOT require any software purchases.
Easy-To-Use
• Plug-n-Play– Plug the camera and stage into the PC.– Download and run the software.
• Automatic Calibration– Stage-to-Pixels– Pixels-to-Microns– Tracking
• Simple functionality is on the main screen.– Advanced Options and tweaks are also easily accessible.
Attaching Your USB Camera( Don’t worry it’ll be on the web page )
1. Open it up. 2. Remove the lens.
3. Add glue. 4. Glue on the C-mount.
Feature Rich• NO Recording Limits
– Unlimited Length (as long as you have space)– ANY Frame Rate & Resolution
• Track EVEN in Difficult Conditions, e.g.:– Young Worms– Thick Food– Contamination– Plate Edges
• Time-Lapse recording.
• An easy pipeline to our Analysis software– Over 100 Features extracted.
More Features• Continually Log the worm’s Real-World Location.
• Snap images in many formats:– JPG, GIF, BMP, PNG
• Advanced control over recording:– Resolution– Video Format– Frame Rate– Time/Frame/Intermittent Lengths
• Advanced control over tracking:– Boundaries– Thresholds– Coordinate stage movements with recording to Minimize Blur
Standardization
• Identical Video & Tracking DataREGARDLESS of the Hardware & OS Configuration
– Allows Searchable Databases of videos & analyses• Dry Lab Experimentation• Phenotypic Identification• Cross-Experimental Comparisons• Meta Studies
• Open Source for reuse (e.g., A Neuronal Imaging Tracker)
Extensive Documentation
• Design overview
• FAQ
• Tutorials
• Troubleshooting guide
• Javadoc Web Pages– ANY Java programmer can Understand, Edit,
& Extend the code– Easy Updates & Maintenance
Example:Supporting a New Motorized Stage
(A Tutorial Document will be Included with the Software)
• Fill in a motorized stage wrapper.– ~5 Lines of Java
• Translate “Move” into the stage’s language– A text command for the serial port.
• ~1 Line of Java
– Or, call the API to move the stage.• A Few Lines of code
The Java Media Framework
• Supports most USB Cameras• Synchronizes multiple data sources
– Cameras, microphones, etc.
• Can Multiplex and Combine data sources Example: 3 synchronized videos– Cyan & yellow filtered fluorescent neurons.– A low magnification worm behavior video.
• Monitor while recording for Real-Time Video Analysis
USBCamera
USBCamera
USBCamera
Worm Tracker 2.0Java
MediaFramework
The Tracking Algorithm
• Convert the image to Grayscale.
• Find the Worm:– Threshold to find the foreground (worm).– Find an appropriate “8-connected” component.
• Find Motion:– Ignore tracked in/out image boundaries.– Subtract successive frames (motion).– Threshold to find movement (worm).– Find large 8-connected components.
• Re-Center the worm upon boundary violation.
Adaptive Thresholding• The Otsu Method
– Assume a bimodal distribution of pixels (worm & background).
– Find a threshold to split the modalities:• Maximize the variance between modalities.• Minimize the variance within modalities.
– O(# of pixels) – Optimal!
8-Connected Components
• 8 Neighbors (vs. 4 – no diagonals)
• “Two Strategies to Speed Up Connected Component Labeling”, 2005, Wu et al.– 1 forward scan– Union find– Decision trees– Sequential memory access
• Area and Boundary discovery during the scan.• O(# of Pixels) – Optimal!
Movement Detection
• Calibrate to Ignore Video NoiseAutomatically establish thresholds:– Minimum area– ∆ pixel value
• Subtract successive Frames– Motion = large 8-connected components
where:| ∆ pixel value | > 0
• Move stage to Keep Motion In Bounds
Acknowledgements
• Chris Cronin
• Ryan Lustig
• Kathleen, Katie, Callie, & Andrew
• Bill Schafer & Paul Sternberg
• Yechiam Yemini (My Dad)
• Zhaoyang (John) Feng
Contact Us
• Email– Ev
– Chris• [email protected]
• WWW– http://sourceforge.net/projects/worm-tracking