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. Background Deoxyribonucleic 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. Background Scanning 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

7. Background Scanning 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

8. 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

9. 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

10. 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

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

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

13. Three Phase Iterative Approach 1 2 3

14. 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

15. Project Timeline We are here.

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

17. 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

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

19. Project Completion We expect to make significant progress on this project, but the problem is too big for “completion” this academic year Upon discovery of verifiable solution, we plan to publish an article in an appropriate journal There will always be more work to do in this relatively infantile field. – Plan: Continue this research at a higher level as a master’s thesis next year at UNH