mBiomechanics research

Individual files are posted in '.txt' format, which may be copied and pasted in MATLAB m-files. The zip archives include multiple m-files and may have sample analyses.
Software development Supported by National Science Foundation Grant IOS-0723288.

Filename	Category	Required toolboxes	Author	Description	Project
coplot	Visualization		W.J. Van Trump	Makes a colormap with a gradient given specified colors.
makeColorMap	Visualization		M. McHenry	Makes a colormap with a gradient given specified colors.	McHenry & Patek (2004)
zKinematics.zip	Kinematics	Image processing	M. McHenry	Used to acquire coordinates describing the midline motion of a swimming fish from an avi movie. This set of m-files are complex and will only be useful for those who have experience with image processing in matlab.	McHenry & Lauder (2005)
videoEdit.zip	Kinematics		M. McHenry	Provides a GUI for very simple video editing.	McHenry & Lauder (2005)
findLandmarks.zip	Morphometrics		M. McHenry	For choosing coordinate points from a photo or AVI video. The old, non-gui version still posted here. Updated 11/6/06.	McHenry (2001)
principleComponents	Statistics	Stats	M. McHenry	Runs a simple principle components analysis for 2 variables including plotting confidence intervals.	McHenry & Patek (2004)
crenshawAnalysis.zip	Kinematics		H. Crenshaw	Provides a number of variables from a 3D trajectoy of motion.	Crenshaw et al (2000)
tracker.zip	Kinematics	Image processing	M. McHenry	Tracks high contrast spot(s). Includes a graphical interface and works on Mac & PC platforms. Videos included for testing. Type 'tracker' at the command line to start. Updated 11/10/06.	McHenry & Lauder (2005)
coordTransforms	Morphometrics		M. McHenry	Three functions that define a local coordinate system from 2 coordinates and calculate the transformations between local and global frames of reference.	McHenry (2001)
CT Processor	Morphometrics		A. Summers	Two GUIs. One calculates the second moment of are for a selected skeletal element in a ct scan. The other shows the dependance of second moment calculations on the threshold that you select for changing the grey scale image into b/w. The file contains a few sample data files from CT scans of the horn shark.	Dean & Summers (2006)
ReducedMajorAxis	Statistics		M. McHenry	Runs a reduced major axis reqression and reports confidence intervals and other stats.	McHenry & Jed (2003)
midline3	Kinematics		A. Summers	Finds the midline of a fish swimming across the field of view. Counts on good contrast and low background noise. Dark fish on light background is required.

The lab uses a number of commercially available software packages for modling, data anlysis, and visualization. These include ADINA for computational fluid dynamics and finite element modeling and MATLAB for analysis and visualization. The following are programs were developed by people in the McHenry Lab.

Program	Author	Description	Download URL
OSIV (Open Source Image Velocimetry)	J. Strother	As its name suggests, OSIV is an open source flow visualization program that analyzes Digital Particle Image Velocitmetry (DPIV) movies to visualize flow fields. It runs on all major platforms and currenly includes a set of fast algorithms. We are currently developing a GUI interface for it.	http://osiv.sourceforge.net/download.html