Image Analysis

SegTrack^{*†}  segmenting and tracking
matlab function library

SASSIGN^{*†}  tracking software based
on softassign matching algorithm
 Costanza^{†}
 Confocal Stack Analyzer Application, plugin for
ImageJ
 CLSM
Tools^{*†}  nuclear segmentation and
lineage analysis
Modeling, Simulation, and Analysis
 xCellerator^{*†}  ODE Based Modeling in Mathematica
 ERLeap^{*†}  Stochastic Simulation (Exact Reaction Leaping)
 SSA^{*†} Stochastic Simulation (Gillespie Algorithm) in Mathematica
 LDSA
 LamDelosme Simulated Annealing in
Mathematica
 Organism^{†}
 ODE based simulation in C++
 mPower^{*†}
 Mathematica wrapper for computational geometry using qhull
 Cellzilla^{*†}
 Static multicellular modeling using Voronoi in Mathematica

PhasePlot^{*†}  Phase portraits in Mathematica
 PPM  Particle Particle Mesh Library  meshing and simulation library of continuous and discrete systems using particlemesh methods.

Tissue3D^{*†}  Mathematica package for
compartmental modeling
 Cellerator†  an
earlier version of xCellerator
 kMech†
 Cellerator plugin for enzyme kineteics
 MathSBML†
 SBML reader and simulator in Mathematica
 Sigmoid†
 Model database and simulation package (uses
Cellerator)
Stochastic Grammars and Model Description
Tools
^{†}Indicates
tools developed by or in collaboration with the
Computable Plant project.
^{*}Indicates Partially or fully funded by
NSF Award 0330786.
Other Useful Software Links:
Computing Frameworks:
Computational Geometry:
revised Mon Jun 1 13:20:03 2009
