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791H Senior Project Proposal

791H Senior Project Proposal. Image Filtering and Enhancement of Scanning Electron Microscope Images Nathan Brouwer Advisor: Rich Messner. Goal. To improve and extract information from DNA images taken by scanning transmission electron microscope (STEM)

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791H Senior Project Proposal

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  1. 791H Senior Project Proposal Image Filtering and Enhancement of Scanning Electron Microscope Images Nathan Brouwer Advisor: Rich Messner

  2. Goal • To improve and extract information from DNA images taken by scanning transmission electron microscope (STEM) • Accomplished with research and use of image processing algorithms

  3. Project Evolution • SURF (Summer Undergraduate Research Fellowship)grant • URA (Undergraduate Research Award) • Honors Senior Project

  4. BackgroundDeoxyribonucleic acid (DNA) • Back Bone • Sugar, Phosphate groups • Nucleotide Pairs • Adenine-Thymine • Guanine-Cytosine Contains Genetic Information *Main Elements: Hydrogen, Carbon, Nitrogen, Oxygen, and Phosphorus *Average distance between base pairs ~.34nm

  5. BackgroundScanning Transmission Electron Microscope • The STEM accelerates an ionized beam of concentrated electrons onto the sample -raster scanning • Electrons travelling through the sample of deflected due to the positive charge of the nuclei of the atoms in the sample • Sensitive Camera detects the received energy at the pixel • Areas with larger nuclei appear as dark spots Maximum Resolution .08 nm

  6. BackgroundScanning Transmission Electron Microscope (Dark Field) • Metal ring just past the sample • Deflected electrons hit the ring and induce a current • The current is proportional to the size of the local nuclei at each pixel • Large nuclei appear of high intensity white spots • This method increases the contrast

  7. Historic Problems with DNA Imaging • Resolution • In recent years STEMs have been developed with high enough magnification (.08nm) • This problem has been theoretically solved • Contrast • DNA consists of molecularly “light” atoms. Electrons aren’t deflected substantially enough to be significantly noticeable

  8. Contrast Problem • ZSGenetics – Danvers, MA (William Glover III, CEO) • ZS has devised methods to bind larger “marker” atoms to certain nucleotide pairs. • Find the markers=find the base pairs • Avg distance between pairs is .34nm • Calculate distance between markers to know the number of pairs between markers

  9. Project Goals • Using a variety of image processing algorithms • Research and Implement a variety of algorithms in MATLAB to extract data in an intelligent and focused manner • William from ZS will be a crucial aid in interpreting images and determining successful algorithms

  10. Possible Algorithms • Basic Techniques • Thresholding • pseudo color mapping • Logarithmic scale stretching • Filtering • Higher Level Methods • maximum entropy method (noise probability estimation)

  11. Pseudo Color Space Mapping This is a rudimentary algorithm that assigns values to colors to better able the user to visualize information

  12. Three Phase Iterative Approach 3 2 1

  13. STEM Training and Data Collection • Travel to Harvard University to take electron microscope safety and operations training • This is a rare opportunity to become EM trained • Provides a more in depth knowledge base on the function and operation of the microscope

  14. Project Timeline We are here.

  15. Budget Note:URA grant has awarded $150 for budget Dell Touch Screen Computer – Cost Share with URA budget and ECE department

  16. Significance • Provide a segue into Graduate Research • Publishable Material-Useful to Engineering and Biochemistry fields • Aid medical research to discover the relationship between genomic variation and disease

  17. Special Thanks • Advisor: Rich Messner • UNH ECE Department • William Glover and ZSGenetics • Daniel Reynolds • Hamel Center for Undergraduate Research

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