PM3 Computational Medicine Laboratory
Our research data and model codes are mostly open source. You may use them without
any guarantees/warranties. Email me with bugs you find. If the code cannot be downloaded,
please email me. All codes and designs are available under suitable licences.
Codes and data
- PM3 SimVascular tar ball.
- Code to generate normally distributed random numbersPage, code
- Human ventricle wedge model: cell to 3D. MPI parallel C codes, under PM3 licence.
- ImageJ/FiJi method for semi-automatic segmentation of liver and kidney: macros and operator instructions
- MATLAB codes for generation of 3D stacks: visualise 3D BF in organs
- 0D whole body circulation model code, model adapted from literature to paediatric case study in 2018
- A computational model for assessment of hepatic and renal blood flow: 3D optimised, code in C
- A computational model for assessment of cardiac blood flow: 3D optimised, code in C
- 2007 3D human atrium model based on explicit finite differences and memory optimisation.
- Mouse SAN model code: Mouse SAN cell model code in C, no dependencies. Email me for a more efficient code, MATLAB code.
- Sensitivity analysis using automatic differentiation and numerical differentiation: Mutual Information and PRCC implementations.
- MATLAB and C codes for eigenvalues of ODEs.
- Uterus cell model code.
- Nelder-Mead simplex parameter optimisation in MATLAB.
- Modified Fenton Karma models for mouse and human SAN codes.
- MATLAB 1D and 2D implicit solvers using alternate directions implicit method (used in Europace 2014)
- MATLAB code for identifying phase singularity/filament. (used for BeatBox and later papers)
- C code for identifying phase singularity/filament.
- BeatBox 2017 paper: BeatBox software.
- Human SAN model for exit pathways data: 3D geometry with tissue types. (Plos ONE 2016)
- Generate vasculature in a 2D/3D volume: C codes with no dependencies. (Frontiers 2018)
- Image processing: Construct 3D model from stacks of tiffs/DICOMS. (MATLAB 2018-ongoing)
- Code for calculating quality of life using real life data from a 2017 study.
- Submission scripts: SHARCNET, Compute Canada, UK EPCC, lfs.
- VTK run time visualisation C and bash.
- Scripts for making line diagrams using MATLAB.
- Human SAN anatomy at various resolutions (0.1 mm, 0.2 mm, original).
- Human ventricle vasculature model (serial and GPU). (Frontiers 2018).
- ImageJ semi-automatic segmentation of liver, brain, kidneys (2018-2019): data and scripts.
- liver, brain, and kidney vascular structures from ateries to arterioles.
- Brain electrical activity: neurons.
- Brain electrical activity: spatially distributed.
- PM3: all above programmes in a tar ball (no guarantees!).
Email: Sanjay Kharche.
Email: Sanjay Kharche.
Data and models
Teaching and for Students
August 5th, 2020. Dr. Sanjay R. Kharche.