Software List

   A list of software packages produced by members of the CSELab:


CIV (version: 1.1, released: February 20, 2014)

Cell Image Velocimetry (CIV) is a MATLAB toolbox that combines cell layer segmentation and image velocimetry algorithms to extract and analyze detailed spatiotemporal information for cell migration, as studied by wound healing assays.

Additional information

CurveletUtils (version: 1.1, released: October 15, 2009)

Matlab source code for a GUI implementing the edge detection method

Additional information

MorphoGraphX (version: 1.0.1256, released: May 6, 2015)

MorphoGraphX is a free Linux application for the visualization and analysis of 3D biological datasets. Developed by researchers, it is primarily used for the analysis and quantification of 3D live-imaged confocal datasets. The first public release of MorphoGraphX is described in this eLife paper

MosaicSuite (version: 1.0, released: July 1, 2016)

MosaicSuite started with a ParticleTracker plugin described in this paper Now it includes several of the image-processing algorithms for fluorescence microscopy available as plugins for the popular free image processing software ImageJ2 or Fiji.

TScratch (version: 1.0, released: May 18, 2010)

TScratch is a software tool to automatically analyze wound healing assays (scratch assays), available as a stand-alone application for Macintosh and Windows and as a source code.

WCCNT (version: 1.0, released: June 23, 2016)

WCCNT is collection of TCL scripts to analyze/visualize trajectories of CNT (carbon nanotubes) and water in VMD


CUBISM-MPCF (version: 1.0, released: April 2, 2013)

C++ framework for developing uniform grid resolution codes

CubismZ (version: 0.9, released: October 11, 2016)

Lossy wavelet-based and lossless high-performance data compression of 3D scientific data

FTLE2D (version: 1.0, released: May 18, 2012)

Code package for computing 2D FTLE fields with support for OpenCL on GPUs

Glycocalyx Structures (version: 1.0, released: February 17, 2014)

Glycocalyx structures

LeSS (version: 1.0, released: July 3, 2009)

LeSS (Leaping Stochastic Simulation) is a C++ software package for simulating chemical reactions.

Additional information

MRAG (version: 1.0, released: October 28, 2014)

C++ framework for developing wavelet-adapted grid codes

Parallel Particle Mesh Library (PPM) (version: 1.2_p1, released: November 12, 2010)

PPM is a software layer between the Message Passing Interface (MPI) and codes for simulations of physical systems using hybrid particle-mesh methods. The library is based on a unifying formulation for the simulations of discrete and continuous systems using particles.

PyMLMC (version: 1.0, released: September 27, 2016)

PyMLMC is a highly modular Python Multi-Level Monte Carlo (MLMC) software targeted at launching and managing Uncertainty Quantification campaigns of deterministic HPC simulation software on super-computers and post-processing the results.

SEM++ (version: 1.0, released: August 14, 2014)

SEM++ contains two implementations of an extended version of the subcellular element method: a C++ version for fast prototyping and a LAMMPS plugin for high-performance computing.

Additional information

uDeviceX (version: 1.0, released: August 25, 2015)

In Silico Lab-On-A-Chip


BASIS (version: 1.1, released: November 3, 2015)

BASIS is a MATLAB package for posterior sampling in parallel, used for Bayesian Uncertainty Quantification and Propagation of complex and computationally demanding physical models.

CMA-ES (version: 1.0, released: June 29, 2009)

The Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Noisy and Global Optimization is an evolutionary (search) algorithm for difficult optimization problems.

Additional information

OpenOpal (version: 1.0, released: July 30, 2009)

OpenOpal is an Open Source software environment for OPtimization And Learning, providing algorithms for automatic optimization, Design of Experiment, and Machine Learning.

Pi4U (version: 1.0, released: January 1, 2015)

Pi4U is an extensible framework for non-intrusive Bayesian Uncertainty Quantification and Propagation of complex and computationally demanding physical models, that can exploit massively parallel computer architectures

smTMCMC (version: 1.0, released: August 1, 2016)

Langevin Diffusion Transitional Markov Chain Monte Carlo