john alan mcdonald: projects

home	2004-05-09

projects

a typical echocardioogram echo segmentation (2004-date) I am currently working on automatic methods for modeling heart anatomy from ultrasound and magnetic resonance images.
wall motion (2002-2003) I model the motion of the left ventricle by fitting periodic time-dependent subdivision surfaces to the trajectories of a number of points on the endocardial surface. The trajectories are obtained from a small magnetic-field-based position and orientation sensor, which is fixed to the end of catheter inserted in the left ventricle and held against the endocardial wall at a number of locations, each for several heart beats. The moving surface is a 2-dimensional subdivision surface embedded in a space of periodic 3D bspline curves, rather than the usual embedding in R³.

ventriculogram segmentation (2001-2003) I recently invented a method for segmenting ventriculograms --- contrast enhanced cine x-rays of the beating heart --- using a boosted decision tree pixel classifier. This is the first method to achieve accuracy comparable to interobserver differences. My implementation, about 320 classes in 80,000 lines of Java, and 1000 lines of C, was delivered to our industrial research sponsor in May 2003.
A patent (McDonald et al, "Segmentation of left ventriculograms using boosted decision trees") is pending. The work will be presented at the SPIE/Medical Imaging conference in San Diego in Feb 2004. Additional publications are pending.

ahn (1999-date) This is my current, comprehensive Java package, for surface fitting, image analysis, and other kinds of scientific computing/data analysis. Approximately 200,000 lines of code, 900 Java classes in 50 packages, using Swing, Java3d, JAI, JMF, RMI, JAF, and JavaMail. This software is the base for almost all current research in the UW Cardiovascular Imaging Lab. Several subsets have been delivered to industrial research sponsors and other licensees.

jtrace (2000-2001) Jtrace is a Java (Swing) based graphical interface used for manual tracing of heart anatomy on 3d ultrasound and other types of medical images. It was primarily written by Loic Yon and Edward L. Bolson. I have responsibility for maintaining the code, which I've modified to work with DICOM images and to improve the user interface.

catfit (1998-1999) Use prior knowledge about expected shape, represented by a shape catalog, to permit rapid and accurate reconstruction from small amounts of irregularly sampled, noisy 3d point data. Intended for use in computer-aided surgery and other medical interventions. Designed, documented, and implemented following ISO 9000-3 and FDA guidelines for software reliability.

lasse (1997-1998) A subdivision surface editor, including data fitting, using Open Inventor, Motif, C++, on various Unix platforms.

xinshi (1991-1997) A package for automatic fitting of labeled piecewise smooth subdivision surfaces to sparse, noisy 3d point data, using C++ and VRML, on various Unix platforms and Win32.

chinese flash (1995-1997) A multimedia computer-aided language learning (CALL) program, for Win16 and Win32 platforms, using Visual Basic 4.0 and 5.0, Visual C++ 4.0 and 5.0, SQL, and MS Access.

mu (1990-1995) A package for interactive visualization and analysis of multispectral image data. Implemented in Common Lisp and C, using low-level X windows operations necessary for real-time performance. Joint with John Adams,Steve Willis, and others at the UW Remote Sensing Laboratory.

announcements (1991-1992) A Common Lisp package for message multicasting, within a multithreaded Common Lisp environment. The Announcements package is a building block of the Prism system for radiotherapy treatment planning. Joint with Mark Niehaus of the UW CSE Dept. and Ira Kalet of the UW Dept of Radiation Oncology.

az (1984-1997) A Common Lisp package covering many aspects of scientific computing, with an emphasis on interactive visualization of high dimensional data.

home Copyright 2004 John Alan McDonald.
All rights reserved.

	echo segmentation (2004-date) I am currently working on automatic methods for modeling heart anatomy from ultrasound and magnetic resonance images.
	wall motion (2002-2003) I model the motion of the left ventricle by fitting periodic time-dependent subdivision surfaces to the trajectories of a number of points on the endocardial surface. The trajectories are obtained from a small magnetic-field-based position and orientation sensor, which is fixed to the end of catheter inserted in the left ventricle and held against the endocardial wall at a number of locations, each for several heart beats. The moving surface is a 2-dimensional subdivision surface embedded in a space of periodic 3D bspline curves, rather than the usual embedding in R³.
	ventriculogram segmentation (2001-2003) I recently invented a method for segmenting ventriculograms --- contrast enhanced cine x-rays of the beating heart --- using a boosted decision tree pixel classifier. This is the first method to achieve accuracy comparable to interobserver differences. My implementation, about 320 classes in 80,000 lines of Java, and 1000 lines of C, was delivered to our industrial research sponsor in May 2003. A patent (McDonald et al, "Segmentation of left ventriculograms using boosted decision trees") is pending. The work will be presented at the SPIE/Medical Imaging conference in San Diego in Feb 2004. Additional publications are pending.
	ahn (1999-date) This is my current, comprehensive Java package, for surface fitting, image analysis, and other kinds of scientific computing/data analysis. Approximately 200,000 lines of code, 900 Java classes in 50 packages, using Swing, Java3d, JAI, JMF, RMI, JAF, and JavaMail. This software is the base for almost all current research in the UW Cardiovascular Imaging Lab. Several subsets have been delivered to industrial research sponsors and other licensees.
	jtrace (2000-2001) Jtrace is a Java (Swing) based graphical interface used for manual tracing of heart anatomy on 3d ultrasound and other types of medical images. It was primarily written by Loic Yon and Edward L. Bolson. I have responsibility for maintaining the code, which I've modified to work with DICOM images and to improve the user interface.
	catfit (1998-1999) Use prior knowledge about expected shape, represented by a shape catalog, to permit rapid and accurate reconstruction from small amounts of irregularly sampled, noisy 3d point data. Intended for use in computer-aided surgery and other medical interventions. Designed, documented, and implemented following ISO 9000-3 and FDA guidelines for software reliability.
	lasse (1997-1998) A subdivision surface editor, including data fitting, using Open Inventor, Motif, C++, on various Unix platforms.
	xinshi (1991-1997) A package for automatic fitting of labeled piecewise smooth subdivision surfaces to sparse, noisy 3d point data, using C++ and VRML, on various Unix platforms and Win32.
	chinese flash (1995-1997) A multimedia computer-aided language learning (CALL) program, for Win16 and Win32 platforms, using Visual Basic 4.0 and 5.0, Visual C++ 4.0 and 5.0, SQL, and MS Access.
	mu (1990-1995) A package for interactive visualization and analysis of multispectral image data. Implemented in Common Lisp and C, using low-level X windows operations necessary for real-time performance. Joint with John Adams,Steve Willis, and others at the UW Remote Sensing Laboratory.
	announcements (1991-1992) A Common Lisp package for message multicasting, within a multithreaded Common Lisp environment. The Announcements package is a building block of the Prism system for radiotherapy treatment planning. Joint with Mark Niehaus of the UW CSE Dept. and Ira Kalet of the UW Dept of Radiation Oncology.
	az (1984-1997) A Common Lisp package covering many aspects of scientific computing, with an emphasis on interactive visualization of high dimensional data.