SimICD: Closed Loop ICD Simulations

Description

This is the codebase for SimICD, a tool for the closed-loop simulation of cardiac EP episodes and virtual ICD logic modeled after the Boston Scientific single chamber transvenous ICD (Boston Scientific). Examples of episode simulations can be found in the paper: ('SimICD: A Closed-Loop Framework for ICD Modelling').

This repository consists of:

A. ICD_Logic:

Contains the sensing and discrimination algorithms for decision-making during simulations, therapy prescription scripts, and calls to and from the simulator to translate the data from the EP simulations into EGMs.

• i. Sensing: Generating EGMs from simulated data and extracting key features.
• ii. Detection: Employing (Boston Scientific) discrimination algorithm to make therapy descisions.
• iii. Therapy: Implementing and analyzing therapy decisions.

B. NSR_Temps:

A template of an EGM representing normal sinus rhythm (NSR) that can be used in morphology analysis.
Users can either use this template or generate their own using a custom mesh, which can be done using the carputils script for NSR provided and passing the results of the simulation using phie_extract.py and generate_egm_from_ascii.m to create a new NSR template.

C. Sim_Files:

Python scripts (using carputils, the Python framework used by OpenCARP - OpenCARP) for running the cardiac simulations. This includes files that simulate both the episode and the ATP therapy applications. These include:

• i. Focal VT
• ii. Re-entrant VT

Users are invited to upload their own meshes, stimulus sites, and electrode sites in order to run simulations. They are also welcome to tailor the simulation scripts to meet their specific experimental requirements.

Table of Contents

• Requirements
• Usage
• Features
• Contact

Requirements

To run this project, the following dependencies need to be installed:

• Python 3.8.10
• MATLAB version R2023b
• pip (Python package manager)
• Linux OS compatibility

Additionally, openCARP and necessary packages must be installed on the machine you are using (including carputils, meshtool, and meshalyzer).
(Details on how to install these can be found on the openCARP website).

Required Files:

To use the example scripts provided, you will need:

• Mesh files (meshname.elem, meshname.lon, meshname.pts, meshname.surf)
• NSR.vtx files (stimulus sites for NSR)
• ATP.vtx (stimulus site for ATP delivery)
• For the Focal VT script, you must also provide the Focal.vtx stimulus site
• electrodesICD.pts (sites within the mesh to record ICD traces)
• input_state.roe (a starting state for your simulation)

Note:

• For details on how to structure the required files, visit the openCARP website.
• The electrodeICD.pts file must be structured in this order: CAN, RVCoil, RVRing, RVTip. (Following the template of electrodes.dat)
• If you wish to structure your electrodes differently, you will need to edit the generate_EGM_from_ascii.m function to match the electrodes you specify for your simulation.

Usage

• To run the scripts, upload the required files mentioned above into the folder of the episode type you wish to simulate. The two generic scripts provided are designed to use the carputils scripts found in Sim_Files.

• Both of these scripts can be run directly in MATLAB (with optional arguments found in the pre-amble of the scripts) using the following commands with your own variable arguments:

1. main_focal.m

matlab -batch 'main_focal(varargin)'

2. main_reentrant.m

matlab -batch 'main_reentrant(varargin)'

Once the simulation is complete, the results will be saved in the OUTPUTS directory.

Features

• Simulation scripts for ventricular arrhytmia episodes
• Therapy scripts for the delivery of ATP
• ICD logic scripts for detection and analysis of episode EGMs
• File Processing functions for extraction and monitoring of data.

Contact

• Any Queries regarding the codebase, please contact: hannah.lydon@kcl.ac.uk
• GitHub: janet-9