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Electronic Imaging for Microscopy - Segmentation Tools Data
Client: U.S. Air Force Research Laboratory - Wright-Patterson AFB
Summary
     The Electronic Imaging for Microscopy project is an initiative designed to modernize data analysis for Materials Science by developing and adapting Signal Processing algorithms towards reducing the human interaction necessary for analysis of digitally acquired image data. Since the development of classical image processing algorithms in the 1970's, many algorithmic approaches have been developed for applications such as medical imaging, homeland security, and computer vision that cannot rely on the intervention of experts to analyze data by hand. Invariably, these algorithms involve (ill-posed) inverse methods that require some prior knowledge of what the structures observed should look like in order to produce reasonable answers. The EIM effort uses Materials Science-specific prior knowledge in order to develop Materials Science-specific algorithms for analysis of microscope-acquired image data to develop realistic models of the structures of the materials examined. These models are useful for subsequent activities such as physics-based forward modeling or developing statistical models of structure. All codes and data are contributed to the greater Materials Science community in order to further the goals of Integrated Computational Materials Engineering as well as reducing the time-to-market for new materials.
     This is a joint effort between the Electronic Imaging and Materials Science communities that is part of the ICMD Tools program at the Materials Directorate of the Air Force Research Laboratory. One of the accomplishments was to push forward the state of the art in expectation-maximization/maximization of the posterior marginals (EM/MPM) segmentation algorithms as it relates to materials systems.
Software
Updated March 8, 2013

Windows XP/Vista/7/8 64 bit
EmMpmWorkbench-v2.112-Win64.zip

Windows XP/Vista/7/8 32 bit
EmMpmWorkbench-v2.112-Win32.zip

OS X 10.6/10.7/10.8 64 bit Intel
EmMpmWorkbench-v2.112-OSX.tar.gz

RHEL 6 x64
EmMpmWorkbench-v2.112-RHEL6-x86_64.tar.gz

Source Code
EmMpmWorkbench-v2.112-Source.zip

Users Manual in PDF Format
Example Data Sets
All Data sets can be found on the Data Downloads page.
Screen Shots
  • Stacks Image 299

    EM/MPM Workbench with Input Image

    Link
  • Stacks Image 300

    EM/MPM Workbench After Segmentation

    Link
Code Availability
All code is available from the BlueQuartz Software Git Repository server.



The code depends on some small parts of boost and for Parallel versions of the code you will need the latest version of Intel Threading Building Blocks (either commercial or open source). In addition to build the Graphical User Interface version of the code you will need Qt version 4.7.x from the Qt Project. This project uses CMake to configure the sources for building.

Documents and Guides
The following documents are being constructed as part of the EIM effort.

Source Code Management - Recommendations for the use of a Source Code Management system when developing computer software.
HTML, PDF

Doxygen Guide - A quick tutorial on the use of the Doxygen commenting system for source codes
HTML, PDF

Software Coding Style - Guidelines for writing more portable software codes using CMake and other accepted
software development practices.
HTML, PDF