ECE U664 --- Biomedical Signal Signal Processing and Medical Imaging
Electrical and Computer Engineering Dept., Northeastern University
Spring 2008
  Professor Dana H. Brooks

• Topics list for this page:
  • Cardiac/neural anatomy
  • EEG programs and data
  • Papers on topics related to EEG's, EP's, brain mapping, etc.
  • Cardiac/neural simulation and visualizations
  • Cardiac cycle animations and tutorials
  • Papers on topics related to ECG's
  • The website for the Sornmo / Laguna book
  • Tutorials, visualizations, and software for Xray CT and other straight-ray tomography
  • Tutorials and visualizations for MRI
  • Tutorial papers and software on medical ultrasound imaging
  • Links for Electrical Impedance Tomography (EIT) and Diffuse Optical Tomography (DOT)
  • Other lists of interest
  • Books and articles of interest
  • Sources of data
• Anatomy of the heart and nervous system / brain:
  • Some nice images of anatomy from a book by Silverthorn, go to http://cwx.prenhall.com/bookbind/pubbooks/silverthorn2/medialib/imagefold.html . and choose different chapters. (To see which chapter is which, go to http://cwx.prenhall.com/bookbind/pubbooks/silverthorn2/ and look at the "Select a chapter" menu. Each topic here leads to a quiz on that chapter.) In particular
    1. CH09 is the central nervous system. (CH08 is the general nervous system). Images 10 and 12 have nice pictures of the function of various areas of the brain. Image 11 has two nice figures to illustrate how we perceive visually what we think we see. Images 14a and b illustrate some aspects of the EEG and the sleep cycle.
    2. CH14 is the cardiovascular system. The various parts of Image 7 show the location and some structures of the heart. The parts of Image 9 show more detail including nice views of the valves. Image 14 shows how the various ion channel openings and closing relate to the cardiac action potential. Image 15c shows how the electrical and mechanical activations are related in time. The various parts of Image 19 show the pattern of electrical activation of the myocardium. Image 22 shows the timing of the various segments of the ECG as related to electrical activation and mechanical contraction. Image 25 shows the cycle of blood flow in the heart as related to valve openings and volume changes. Image 27 shows a chart realting ECG, pressure, heart sounds, and left ventricular volume.
  • Another link for nice cardiac and thoracic anatomical images: http://info.med.yale.edu/intmed/cardio/imaging/ . If you select the right arrow at the top you get links to lots of anatomical images of different physiolgoical systems.
    
    
• EEG programs and data
  • A well-known open-source Matlab program for processing EEG, EP, and some other kinds of data is EEGLAB.
  • The rest of these I've collected but don't know much about; however some of them may be worth exploring:
  • Laboratory for Intelligent Imaging and Neural Computing
  • BCI (Brain Computer Interface) Competition 2003 (the last time this competition was run as far as I know)
  • Wadsworth BCI Dataset
  • Experimental Brain Computer Interface Software for the ModularEEG
  • The OpenEEG project (Claims to tell you how to build your own EEG device and software)
    
    
• Papers on topics related to EEG's, EP's, brain mapping, etc.
  
  
  • Baillet, Mosher, and Leahy, Electromagnetic Brain Mapping, IEEE Sig Proc Mag 18:6, pp. 14-30, Nov. 2001, a nice tutorial article on this topic; we used one figure from it in our discussion of the source of EEG signals.
  
  
  
• Cardiac and neural simulation and visualization programs:
  • A great package to understand the relationship between cardiac electrical activity and how the ECG looks is ECGSim, http://www.ecgsim.org , written by Thom Oostendorp and Adriaan van Osteroom. I plan to have you all use this program for our computer assignment on ECG's.
  • A paper describing ECGSim by the program's authors is here and a tutorial on how to use it is here .
  • The visualization program we will use in class to show cardiac electrical maps is available on-line: http://www.sci.utah.edu/cibc/software/map3d.html.
  • A FitzHugh-Nagoma model of activation: http://stardec.hpcc.neu.edu/~fenton/java/2dfhn.html .You can change the conduction behavior of a region which will cause a spiral wave behavior. (Interesting note: I'm guessing from the URL that the author is a guy named Flavio Fenton who did his Ph.D. in the NU Physics Dept. working with Alain Karma.)
  • A program for simulation of cardiac propagation using cellular automata, available for both Windoze platform and for the Max/OSX . The original home of this CESLab project seems to have disappeared but these downloads seem to be available.
  • Here's one for neural simulations: An interactive model of squid axon by Semahat Demir: http://ssd1.bme.memphis.edu/icell/squid.htm .It's part of her iCell Modeling Software.
    
    
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• Animations of cardiac electrical / mechanical activity and some tutorial material on how the cycle works:
  • A nice animation of cardiac mechanical and electrical behavior: http://www.phschool.com/science/biology_place/biocoach/cardio1/pump.html . The tabs on the left side of this page actually work through a decent tutorial of the whole mechanical and electrical cycle.
  • Heart cycle animation . This animation requires the Shockwave Flash plugin, and you can download the player plug-in from www.macromedia.com/software/flash.
  • Tutorial on ischemic heart disease
  • ECG basics and analysis from the University of Utah.
  • A nice introduction to ECG interpretation from NYU med school, written by Henry Feldman (who I'm guessing is the son of a retired professor formerly in our department!): http://students.med.nyu.edu/erclub/ekgexpl0.html .
  • Another description of ECG interpretation with lots of examples is at http://www.ecglibrary.com/ecghome.html ., which also contains a nice history of the ECG.
  • A series of webpages with descriptions of various cardiac electrophysiological disorders: Cardiovascular Physiology Concepts.
  • A detailed introduction to Membrane Transport and Bioelectric Activity: http://imc.meded.com/integrated/demos/hpdemo/program/section1/1outline.htm .
    
    
• Papers on topics related to ECG's
  
  
  • Circulation article by Hurst on the naming of ECG waves (Circulation. 1998;98:1937-1942.): http://circ.ahajournals.org/cgi/content/full/98/18/1937.
  • From the Jan. 1997 IEEE Signal Processing Magazine, Brooks and MacLeod, Cardiac Electrical Imaging . My favorite (in an unbiased way of course) introduction to the topic ...
  • A very recent paper by Natalia Trayanova from John's Hopkins on mechanisms of defibrillation based on results from modelling studies is here ,
  • A long review article on implantable defibrillators by Swerdlow and Friedman from Dec. 2005 is here.
  • A short (2-page) article comparing different QRS detectiion schemes, from 2003, is here.
  • A 1990 IEEE Transactions on Biomedical Engineering article comparing noise sensitivity of 9 QRS detectors in here .
  • A 1991 IEEE Transactions on Biomedical Engineering article on a filter-bank approach to QRS detection is here .
  
  
  
• The website for the Sormo-Laguna book is here.
  
  
• Tutorials, visualizations, and software for Xray CT and other straight-ray tomography
  • Two animations of Filtered Back-Projection type reconstructions are here for the Shepp-Logan Phantom and here for a torso slice.
  • Prof. Jeff Fessler's web page at U Michigan. It includes links to some interesting articles and also to free software for simulation and reconstruction of Xray CT and other straight-ray tomography problems and some associated processing algorithms.
  
  
  
• MRI: On-line tutorials, some with nice visualizations:
  • Animated intro to MRI . This has some great visualizations. Note that it requires Shockwave to run.
  • More text and more detail but also some useful graphics and animations. For this one be sure to click on the little boxes and arrows in the text to see graphs and animations (respectively).
  • Another intro guide to lots of aspects of MRI, somewhat less interactive and detailed than the previous ones.
  • A chart of tissue type vs. T1 and T2 contrast.
  • More on T1 and T2 including a whole pile of illustrations of how different weighting makes a difference in the resulting images.
  • Some powerpoint slides, designed as an intro to functional MRI (fMRI) but with some very nice information on T1 and T2 phenomena and imaging
  • A guide to how to simulate the Bloch equations, complete with Matlab code if you are really into it. I haven't tried it so don't know how good it is.
  • The technology website of the International Society for Magentic Resonance in Imaging (ISMRM), the society of the pro's in this field. Click on the Education link on this site for lots more links to stuff.
  • A webpage with lots of links to stuff MRI.
  
  
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• Tutorial papers and software on medical ultrasound imaging
  • A paper from the IEEE Engineering in Medicine and Biology Society Magazine from 2000 Current Status and Future Technical Advances of Ultrasonic Imaging, by P.N.T. Wells
  • A much longer tutorial paper from Reports on Progress in Physcis (Rep. Prog. Phys.) from 1999, Ultrasonic imaging of the human body, by the same author, P.N.T. Wells
  • Another tutorial on medical ultrasound from the British Journal of Radiology from 1997, New and future developments in ultrasonic imaging by T.A. Whittingham
  • A more mathematical paper that looks at how to model the fields generated by ultrasound, by Jorgen A. Jensen, the author of the Fields II ultrasound simulation program linked below, Ultrasound imaging and its modeling
  • An article about the development and directions of ultrasound beamformers which has nice images to help understand what is going on is here.
  • A short tutorial paper from the IEEE Signal Processing Society Magazine from 1997 with an orientation towards practical considerations by someone in industry, Signal Acquisition and Processing in Medical Diagnostic Ultrasound by Jens U. Quistgarrd
  • A Matlab, freely-available simulation program for ultrasound propagation that is widely used in both industry and academia is Fields II, by Jorgen A. Jensen (again). There is also some tutorial material and a whole page of links to papers available off that site too.
  
  
  
• Links on Electrical Impedance Tomography and Diffuse Optical Tomography (DOT)
  • A general EIT website.
  • Electrical Impedance Imaging Laboratory at Rensellear Politechnic Institue (RPI)
  • Photon Migration Imaging Lab (DOT) at Mass General Hospital; includes several open-source software packages.
  • EIDORS, a Matlab package for both EIT and DOT
  
  
  
• The source for much of this material is:
  • Rob MacLeod's course web page: http://www.cvrti.utah.edu/~macleod/bioen/be6460/ . Lots of good stuff there, much of it repeated below.
  • Rob MacLeod's background links page where I got a lot of this stuff: http://www.cvrti.utah.edu/~macleod/bioen/be6000/background.html .
    
    
• Books and articles:
  • The Bioelectromagnetism book by Malmivuo and Plonsey is available http://butler.cc.tut.fi/~malmivuo/bem/book/index.htm .
  • The classic book on tomography, which we will use extensively, Principles of Computerized Tomographic Imaging, by Kak and Slaney, is available on-line: http://www.slaney.org/pct/pct-toc.html .
  • Some notes on iterative solutions to linear systems.
    
    
• Sources of data
  • Physionet, http://www.physionet.org/ Important data source which contains a large number of datasets to download.
    • The start of their tree for finding datasets is Physiobank, http://www.physionet.org/physiobank/
    • The actual index of their archived datasets is http://www.physionet.org/physiobank/database/
    • Their list of other databases is http://www.physionet.org/physiobank/other.shtml
  • One interesting library of ECG datasets (a link to which is also available off Physionet, as well as above under tutorial material on the ECG) is http://www.ecglibrary.com/ecghome.html