791H Senior Project Proposal

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Oct 29, 2013 (3 years and 9 months ago)

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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)



Accomplished with research and use of image
processing algorithms


Project Evolution


SURF (
Summer Undergraduate Research
Fellowship)grant




URA (Undergraduate Research Award)




Honors Senior Project

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



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

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

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

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

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

Possible Algorithms


Basic Techniques


Thresholding


pseudo
color
mapping


Logarithmic scale stretching


Filtering



Higher Level Methods


maximum entropy
method (noise probability estimation)

Pseudo Color Space Mapping

This is a rudimentary algorithm that assigns values to
colors to better able the user to visualize information

Three Phase Iterative Approach

1

2

3

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

Project Timeline

We are here.

Budget

Note
:
URA

grant

has

awarded

$
150

for

budget

Supplies

Paper


Color Printing

2 Reams

$35.98



Flash Drives


8 GB

2

$39.98

Travel

Durham
-
Danvers

96 mi RT

2 Trips

$48.00



Durham
-
Cambridge

138 mi RT

3 Trips

$103.50

Other Expenses

Photo Copies



250

$25

Total







$252.46

Dell Touch Screen Computer


Cost Share with URA budget
and ECE department

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

Special Thanks


Advisor: Rich
Messner


UNH ECE Department


William Glover and
ZSGenetics


Daniel Reynolds


Hamel Center for Undergraduate Research