Awesome list for Computational Physiology

Here we would like to collect links to everything that you find awesome. If you wonder what an awesome list is you can checkout github.com/sindresorhus/awesome.

Image processing

• MeVisLab - a powerful, modular framework for image processing research and development with a special focus on medical imaging

• VMTK - collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels

• ITK - The toolkit provides leading-edge segmentation and registration algorithms in two, three, and more dimensions

• Seg3D - Seg3D combines a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit.

Mesh generation

• GMSH - A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities

• CGAL - CGAL is a software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library

• TetGen - A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator

• Cleaver - A multimaterial tetrahedral meshing library and application

Gemetric modeling

• Blender - open source modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation

Optimization

• pagmo - pagmo is a C++ scientific library for massively parallel optimization

• pygmo - pygmo is a scientific Python library for massively parallel optimization based on pagmo.

• pymo - Multiobjective optimization in python

• NLopt - NLopt is a free/open-source library for nonlinear optimization,

• Ipopt - Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization

• Optizelle - An Open Source Software Library Designed To Solve General Purpose Nonlinear Optimization Problems

• Moola - A set of optimisation algorithms specifically designed for PDE-constrained optimisation problems to be used with dolfin-adjoint.

Simulation software

General

Finite element

• FEniCS - Open source computing platform for solving PDEs in Python
• OpenCMISS - Modelling and visualisation for complex bioengineering problems.
• BVPy - Bvpy is a python library, based on FEniCS, Gmsh & Meshio, to easily implement and study numerically Boundary Value Problems and Initial Boundary Value Problems through the Finite Element Method.

Finite Volume

• OpenFoam - Open source CFD software

Cardiac mechanics

• pulse - Cardiac mechanics simulator based on FEniCS

• pulse-adjoint - Data assimilation tool based on pulse

Electrophysiology

• CBCBeat - an adjoint-enabled framework for computational cardiac electrophysiology

• CARP

• openCARP - open source version of CARP

Electromechanics

• SciRun - Problem solving environment for modelling, simulation and visualization

• Chaste - Cancer Heart And Soft Tissue Environment

Cellular modeling

• gotran - Library for declaring ODEs

• Myokit - Python based software package designed to simplify the use of numerical models in the analysis of cardiac myocytes.

Model repositories

• CellML - Cell models

• BioModels - Repository of mathematical models of biological and biomedical systems.

Visualization

• Paraview - open-source, multi-platform data analysis and visualization application.

• VTK - The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing, and visualization

• ImageVis3D - Volume rendering program

• FluoRender - Interactive tool for multi-channel fluorescence microscopy data visualization and analysis

• Map3D - Scientific visualization application to display and edit complex, three-dimensional geometric models and the scalar data associated with those models. The map3d interface provides interactive display of both geometry and data assigned to elements of that geometry