Recognition, Tracking, and Data Acquisition for Microscopic Worms
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Transcript of Recognition, Tracking, and Data Acquisition for Microscopic Worms
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Recognition, Tracking, and Data Acquisition for Microscopic Worms
ECPE 491: Senior DesignProfessor Mani Mina
Client: Dr. Santosh Pandey, Microfluidics Lab
Graduate Supervisor: Roy Lycke Ryan Alley, Team Leader Colin Ray, Communicator Laith Abbas, Webmaster Shan Zhong Shusheng Xu
Group 03: Worm Tracking
Background C. elegans
What are C. elegans? Why are C. elegans useful? How are C. elegans studied?
Behavior Qualitative vs. quantitative data How to gather quantitative data?
Problem Statement
Group 03: Worm Tracking
Academic research MBFBioscience—WormLab Similarities between existing solutions Distinguishing characteristics
Market SurveyGroup 03: Worm Tracking
The software shall support the following video compression codecs:
Microsoft Video 1 Intel Indeo
The software shall support input video frame-rates between 1 and 30 frames-per-second.
The software shall prompt the user to enter video parameters.
The interface shall support singular and batch selection and processing of video files.
Functional Requirements
Group 03: Worm Tracking
Upon completion of analysis, the software shall provide a confidence level in its worm assessments, based upon video quality (resolution, noise, etc..).
The software shall identify C. elegans with a success rate of at least the aforementioned confidence level, as confirmed by human judgment of the video*. In addition, it shall not give a false-positive for any non-worm artifact.
Functional Requirements
Group 03: Worm Tracking
*A bed of test-bench videos shall be chosen for this assessment by the client, Selected to test a variety of situations
Analysis shall provide, at a minimum, the X-Y coordinates of worm centroid, head, and tail over the duration of a given video, as well as the derived velocity and acceleration from the aforementioned worm data.
Additionally, the analysis shall also fit a spline to each worm’s curvature for each frame and present this spline graphically.
Functional Requirements
Group 03: Worm Tracking
The software shall be well-documented The software shall run on the target
computers without additional hardware The software shall be easy-to-use by a
lab technician The software shall process video at no
less than 10 MB of video data per second The software and any support files shall
be wrapped in a single installer
Non-Functional Requirements
Group 03: Worm Tracking
Input videos must be a minimum of 20 frames in length.
No more than five worms per unit volume (1 cm x 1 cm x 100 microns).
Potential Risks In the case that our software fails, data
will have to extracted from the video manually.
Non-Functional Requirements
Group 03: Worm Tracking
Typical Usecase: Lab technician records videos, noting
magnification and scale Lab technician starts program, is
prompted for file(s) and relevant information (magnification and scale)
Video is analyzed by software and outputs data as file, informs user
System DesignGroup 03: Worm Tracking
Details
Detailed DesignGroup 03: Worm Tracking
Currently reads and processes pre-recorded video
Performs background subtraction Finds centroid and outputs coordinates to CSV Graphically fits spline Limitations:
Number of worms No collision-detection
TODO: add screenshots~!
Prototype Group 03: Worm Tracking
Ryan Alley Interface Description, Methodology
Colin Ray Video Input Layer, Background Subtractor
Laith Abbas Webpage, Documentation
Shan Zhong Centroid Finder, Spline Fitting
Shusheng Xu Centroid Finder, Spline Fitting
Individual Contributions
Group 03: Worm Tracking
Play a video!!!! Metrics (human comparison, quality of
videos, etc…)
Test Plan Group 03: Worm Tracking
Hardware purchase not considered. Open-Source platform provides free
license. Labor… free.
Cost EstimateGroup 03: Worm Tracking
Prototype version 1.0 implemented Lessons learned:
Need to further explore potential algorithms
Frame-by-frame processing Model-based approach
Image analysis utilities
Project StatusGroup 03: Worm Tracking
Gantt chart.
Project Milestones
Group 03: Worm Tracking
References Group 03: Worm Tracking