Determine new application spaces in the sequencing platform using visions systems

1
Determine new application spaces in the
sequencing platform using visions systems

• Jessica Perez
• Summer Research Program in Genomics
• Massachusetts Institute of Technology
• Summer 2007

2
Outline

• Approach and Goals
• Vision Systems
• Potential Application Spaces
• Demonstrated Application Spaces

3
Project Overview

• Approach use Cognex Smart Sensor and Intellect
  1.4.0 software as a model to demonstrate the
  capabilities of vision systems
• Goals
• Explore capabilities of software
• Look for application spaces
• Take application and prove principal

4
Vision Systems

• Software Capabilities
• Lighting
• Post Processing

5
Software Capabilities

• Blob Identification

• 1D Bar Scanning

Flexible Flaw Detection
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User Interface
Tool Box
Viewing Screen
Result Table
7
Blob Identification
IDENTIFICATION CRITERIA
Area Average Intensity
Darker Objects Meet Parameters
Lighter Objects FAILED
8
1D Code Reader
Numerical Code Read PASS
9
Flaw Detection
PARAMETERS
Blob Color Area Perimeter
Model
10
Additional Tests
Counting
Filtering
TOOLS
Measurement
Optical Character Recognition Reader
2D String Reader
11
Lighting
Geometry
Filtering
Intensity
Answer.com
12
Common Lighting Techniques
 Bright Field
 Dark Field
 Back Lighting
From Vision Light Tech
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Post Processing

• MatLab Histogram Filter

Before
After
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Potential Application Spaces

• Process Solexa Screening
• Consumer Glass Tubes

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Process Solexa Screening

• Quality Control Check in the Solexa Sequencing
  Process

Flowcells
Clusters
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Proof of Principle

• Blobs represent clusters of DNA

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Consumer Test Tube
Probe
Sonication
Sonic Waves
DNA
18
Backlighting
BEFORE
Detection of Dimensions and Shape of Transparent
Objects
AFTER
Images by Keyence-Engineering Knowledge
19
Setup Components
LED Strobe Light
Diffuser
Magnification Lens
20
Setup
21
Finish Product
Tube under Backlighting
Distance to be measured
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Conclusion

• Vision systems have unlimited potential
• Implementation of vision systems will improve the
  efficiency at various stages of the sequencing
  process.

23
Acknowledgements

• Technology Development Group
• Eva Markiewicz
• Shailendra Yadav
• Filip Rege
• Andrew Barry
• Todd Sparrow
• Tracey Honan
• Pat ___

• Directors of Education
• Shawna Young
• Dedric Carter
• Eric Lander
• Broad Institute