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Awesome list for Computational Physiology

10
GitHub Stars
45
Curated Resources
10
Categories
23 hours ago
Last Refreshed
Image processingImage SegmentationMesh generationGemetric modelingOptimizationSimulation softwareModel repositoriesVisualizationMeshesOpen Data

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What's inside

Model repositories

  • BioModels

    Repository of mathematical models of biological and biomedical systems.

  • CellML

    Cell models

Gemetric modeling

  • Blender

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

Simulation software

  • BVPyGeneral

    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.

  • CBCBeatElectrophysiology

    an adjoint-enabled framework for computational cardiac electrophysiology

  • ChasteElectromechanics

    Cancer Heart And Soft Tissue Environment

  • circulationCardiac mechanics

    0D/1D blood flow simulator

  • FEniCSxGeneral

    Open source computing platform for solving PDEs in Python

  • FEniCSx-beatElectrophysiology

    Cardiac electrophysiology simulator based on FEniCSx

Mesh generation

  • CGAL

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

  • Cleaver

    A multimaterial tetrahedral meshing library and application

  • fTetWild

    A high-quality tetrahedral meshes generator

  • GMSH

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

  • MyoMesh

    A pipeline for generating patient-specific heart meshes and converting them to a format suitable for electrophysiological simulations

  • TetGen

    A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator

Image Segmentation

  • DeepValve

    Automatic detection pipeline for the mitral valve in 4ch CMR.

Visualization

  • FluoRender

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

  • ImageVis3D

    Volume rendering program

  • 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

  • Paraview

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

  • Plotly

    Nice visualizations of plots.

  • VTK

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

Meshes

  • Four-chamber heart meshes

    A publicly available virtual cohort of four-chamber heart meshes for cardiac electro-mechanics simulations

Optimization

  • Ipopt

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

  • Moola

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

  • NLopt

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

  • Optizelle

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

  • 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.

Showing a sample of 45 resources. View the full list on GitHub →