IPRO 313

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IPRO 313 Development and Documentation of
INtegrated Saxs ANalysis Environment (INSANE), a
Computational Environment for the Analysis of
Small Angle X-Ray Scattering (SAXS) Data at
BIOCAT
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Statement of Purpose
This project seeks to develop a user-friendly,
computational environment for rapid and
sophisticated analysis of small angle x-ray
scattering (SAXS) data at the BIOCAT beamline at
Argonne National Lab.
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Background Information
Theory
sample
Camera
X-ray
CCD
Beam stop
Scattered x-rays
Sample Image

• X-rays interact and scatter off electrons in
  sample.
• X-rays are high energy and scatter little
  resulting in small scattering angles.
• A long camera is used to read the small angles.
• X-rays are detected by the CCD and an image is
  sent to a computer.
• Information about the sample can be determined
  from the resulting image.
• The scattering angle is determined from the
  distance between pixel and center.
• The scattering angle is to determine properties
  of the shape of the molecule.

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• What does the data look like?
• What can be determined from the data?

Guinier Plot Allows for the Rg values to be
calculated Information on Shape
Long Camera Image of Sample (large image) and
Silver behenate (small image)
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Background Information
Current Analysis Techniques

• Several programs are available for analysis
• Fit2D
• Cumbersome, Not User Friendly
• User Masks by Hand
• User Defines Beam Center
• Chooses bright spots, by eye
• User Imports/Exports Data by hand to Excel
  spreadsheet
• IGOR-Pro

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Our Approach

• Development of the Documentation
• 3 Major Audiences
• Software Developers
• Novices
• Experienced Users

How do we reach all three audiences through one
document?
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Development of Documentation (contd)
Web-based document with information pertinent to
all three groups contained within.
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Development of Documentation (contd)

• Documentation Contents
• SAXS Theory
• Current Analysis Techniques
• Software Design Plans
• Information on the Algorithms
• Help File
• Links to our software and other analysis programs

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Development of INSANE software package

• Initial Phase
• Development of a GUI that can
• Import file from data acquired at BIOCAT
• Convert from .smv format to .tif format
• Find Beam Center
• Implement the mask
• Perform Radial Integration

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INSANE software package
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INSANE Software Package
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INSANE Software Package
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INSANE Software Package
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Accomplishments

• Documentation
• Web-based document has been completed
• Software
• Algorithms
• Beam Center, Masking, Radial Integration
• Conversion of an Image from .smv to .tif

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Problems Encountered

• Documentation development
• Converting .SMV files to .tif files
• Algorithm Development
• Merging Algorithm
• Masking Algorithm

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Future Goals

• Documentation
• Ability to Search
• Algorithms used
• Step-by-Step Instructions
• Software
• Integrated Software Package with ability to
  analyze SAXS data

Sample Image
3-D structure
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Acknowledgements
We would like to thank Dr. Tom Irving, Dr. Nick
Menhart, and Ahmed Mirza for demonstrating
various aspects of SAXS theory as well as
reviewing the documentation. We would also like
to thank Jaby Jacob for providing a demonstration
of IGOR-Pro.
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Team Members
Advisor Dr. Nick Menhart Team Leader Ali Aga
(EE/CPE) Documentation Group Ryan Pendleton
(MBB), Nathan Yardley(MBB), Ronak Desai(MBB), and
Brad Lunde (MBB) Software Group Ken McIvor
(CPE), Ali Aga (EE/CPE) Syed Sheeraz (CS), Ken
Mcivor (CS), Prasad Ullal (CS), Adit Ranchal
(CPE), Mark Mika (MME)