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Awesome

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awesome

Awesome list for Computational Physiology
https://github.com/ComputationalPhysiology/awesome

Last synced: 14 days ago
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  • Gemetric modeling

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

  • 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
    • VMTK - collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels
    • Seg3D - Seg3D combines a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit.
    • saxomode - open-source toolkit for 3D ventricular shape analysis from cardiac magnetic resonance short axis view medical images.
    • MeVisLab - a powerful, modular framework for image processing research and development with a special focus on medical imaging
    • ITK - The toolkit provides leading-edge segmentation and registration algorithms in two, three, and more dimensions

  • Image Segmentation

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

  • Meshes

    • Cellular modeling

      • Four-chamber heart meshes - A publicly available virtual cohort of four-chamber heart meshes for cardiac electro-mechanics simulations https://doi.org/10.1371/journal.pone.0235145

  • Mesh generation

    • MyoMesh - A pipeline for generating patient-specific heart meshes and converting them to a format suitable for electrophysiological simulations
    • Cleaver - A multimaterial tetrahedral meshing library and application
    • MyoMesh - A pipeline for generating patient-specific heart meshes and converting them to a format suitable for electrophysiological simulations
    • 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
    • fTetWild - A high-quality tetrahedral meshes generator

  • Model repositories

    • Cellular modeling

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

  • Open Data

    • Cardiac MRI

      • M&Ms-2 - **Various RV and LV pathologies, healthy subjects**. 200 annotated images from four different centers, segmented by experienced clinicians, including contours for the left (LV) and right ventricle (RV) blood pools, as well as for the left ventricular myocardium (MYO).

  • 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,
    • 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
    • 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.
    • pymo - Multiobjective optimization in python

  • Simulation software

    • Cardiac mechanics

      • pulse - Cardiac mechanics simulator based on FEniCS
      • circulation - 0D/1D blood flow simulator
      • fenicsx-pulse - Cardiac mechanics simulator based on FEniCSx

    • Cellular modeling

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

    • Electromechanics

      • SciRun - Problem solving environment for modelling, simulation and visualization
      • Chaste - Cancer Heart And Soft Tissue Environment

    • Electrophysiology

      • CARP
      • openCARP - open source version of CARP
      • FEniCSx-beat - Cardiac electrophysiology simulator based on FEniCSx
      • CBCBeat - an adjoint-enabled framework for computational cardiac electrophysiology

    • General

      • 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.
      • MonoAlg3D
      • OpenCMISS - Modelling and visualisation for complex bioengineering problems.
      • MonoAlg3D

  • Visualization

    • Cellular modeling

      • 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
      • 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
Programming Languages
Python 3 C++ 2 C 1
Categories
Simulation software 16 Optimization 8 Image processing 7 Mesh generation 7 Visualization 5 Model repositories 3 Open Data 1 Image Segmentation 1 Gemetric modeling 1 Meshes 1
Sub Categories
Cellular modeling 12 General 4 Electrophysiology 4 Cardiac mechanics 3 Electromechanics 2 Cardiac MRI 1
Keywords
visualization 1 scientific-visualization 1 scientific-computing 1 scientific-computations 1 qt6 1 qt5 1 python 1 open-source 1 mesh-generation 1 linear-systems 1 inverse-problems 1 forward-problem 1 dataflow-programming 1 cmake 1 c-plus-plus 1 boost-libraries 1 biomedical 1 simluation 1 medicine 1 hearth 1 cuda-libraries 1 parsing 1 parser 1 ode 1 gotran 1 code-generation 1