Introduction
Caenorhabditis Elegans (C. Elegans): "is a free-living, transparent nematode (roundworm), about 1 mm in length, which lives in temperate soil environments" (Wikipedia).
C.Elegans attracted many scientists due to their biological properties. After many studies and researches These worms were considered to be model organisms. Organisms are recognized as model organisms due to their unique biological behaviors. C. Elegans are considered special for numerous reasons.First of all they are a multicellular eukaryotic organisms, they are simple but they also offer a large pile of data to be studied and analyzed.In addition, they are also the simplest organisms that has a nervous system. Due to that and because they have transparent bodies it makes it simpler to study their cellular differentiation.
Considering the unique physical qualities these organisims posses. Many scientists are studying the behavior of these worms. To do so an automated tracking system needs to be created. The system should be able to track the behavior of the worms after a certain experiment is done. All tracking will be done on prerecorded videos of the experiment. In addition, the system must be able to analyze and provide statistical data that describes the behavior of the worms.
C.Elegans attracted many scientists due to their biological properties. After many studies and researches These worms were considered to be model organisms. Organisms are recognized as model organisms due to their unique biological behaviors. C. Elegans are considered special for numerous reasons.First of all they are a multicellular eukaryotic organisms, they are simple but they also offer a large pile of data to be studied and analyzed.In addition, they are also the simplest organisms that has a nervous system. Due to that and because they have transparent bodies it makes it simpler to study their cellular differentiation.
Considering the unique physical qualities these organisims posses. Many scientists are studying the behavior of these worms. To do so an automated tracking system needs to be created. The system should be able to track the behavior of the worms after a certain experiment is done. All tracking will be done on prerecorded videos of the experiment. In addition, the system must be able to analyze and provide statistical data that describes the behavior of the worms.
Functional Specification
Video Support
- The software shall support the following video compression codecs
- Microsoft Video 1
- Intel Video
- The software shall support input video frame rates between 1 and 30 frames-per-second.
Interface
- The software shall provide a graphical user interface that allows the user to select worms and track only data for the selected worm(s)
- The interface shall prompt the user to enter video parameters
- This feature shall be easily scalable to accept a wide range of parameters.
- The interface shall support batch processing of multiple video files
Tracking
- The tracking system shall identify C. Elegans in pre-recorded videos with a 99% success rate, as confirmed by human judgment of the video.
- The tracking system shall filter out background noise that could be incorrectly identified as a worm, including, but not limited to, walls and shadows
- The software shall provide a confidence interval for worm identification after the event of a worm collision based on the frame rate.
Frame Rate per Second | Confidence Interval |
---|---|
1-5 | 50% |
6-10 | 75% |
11-20 | 90% |
21-30 | 99% |
Data
- The analysis system shall provide X-Y coordinates of worm centroid, head, and tail over the duration of a given video
- The analysis system shall be able to derive velocity and acceleration from the mentioned worm data
- The analysis position shall be extrapolated as a spline vector for each frame, with interpolations given between frames
- The analysis system shall draw worm location and movement graphically on the video frame after it has been processed
- The analysis system shall identify each selected worm's state of locomotion over time
Non-Functional Specification
- The software shall process video at no less than 1 GB of video data per minute
- The software and any support files shall be wrapped into a single installer