automated tracking of biological cells · powerpoint presentation author: lrice10 created date:...
TRANSCRIPT
![Page 1: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/1.jpg)
Automated Tracking of
Biological Cells
Lance Rice
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![Page 2: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/2.jpg)
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Automated Cell Tracking
• Biological cell cultures
• Prerecorded microscopy
video
• Maintain location of
every cell over entire
video
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Why it Matters
• Incredible Amount of
o Diversity
o Volume
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Toxins
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Toxins
Ecological Factors?
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(100 clicks) x (1000 frames) x (12 Videos) =
1.2 MILLION CLICKS!
(Recorded experiments) x 12
• ~100 cells
• ~1000 frames
• Efficiency
• Accuracy
• Completeness
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Method Overview
• Detection
• Association (Low)
• Association (High)
Position
Time
Cell1 Cell2
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Challenges
• Detection
o Missed Detections
Position
Time
Traffic!!
![Page 9: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/9.jpg)
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Challenges
• Detection
o Missed Detections
o Detection noise
Position
Time
Are we positive that cell-1
went to the right?
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Challenges:
• Detection
o Missed Detections
o Detection noise
• Association
o Incorrect Matches
Position
Time
ID Switch!
![Page 11: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/11.jpg)
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Challenges:
• Detection
o Missed Detections
o Detection noise
• Association
o Incorrect Matches
o Failed to make any connection
Position
Time
Fragments!
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Detection
Experimented with 3 approaches
Wrong!
1. Circle Fitting
Correct Answer Result
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Detection
Wrong!
1. Circle Fitting
2. Watershed
Correct Answer Result
![Page 14: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/14.jpg)
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Detection 1. Circle Fitting
2. Watershed
3. Distance Fitted Ellipse
Correct Answer
![Page 15: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/15.jpg)
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Association
Position
Size
Motion Pattern
Appearance
Gab
Connections
Low Level High Level
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![Page 18: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/18.jpg)
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![Page 19: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/19.jpg)
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Results (cont.)
0
Circle Fitting Watershed Distance Fitted Ellipse
![Page 20: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/20.jpg)
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Conclusions
• P. Parvum tracking on low quality video
• Improvements through better Detection
• Problem areas
o False Positives & ID switches
o Dropped tracks
![Page 21: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/21.jpg)
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The Next Step
Trained Detector
o Expand on variety of data
Area ?
Color ?
Shape ?
Proximity ?
![Page 22: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/22.jpg)
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The Next Step
• Visualization of cell motion patterns
![Page 23: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/23.jpg)
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The Next Step
• Cluster analysis
![Page 24: Automated Tracking of Biological Cells · PowerPoint Presentation Author: Lrice10 Created Date: 9/16/2013 4:31:20 PM](https://reader033.vdocument.in/reader033/viewer/2022050103/5f41d2c71dbd52223040fa4f/html5/thumbnails/24.jpg)
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Thank you
Questions?