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