Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and...

Area of Science:

• Biomedical Engineering
• Computational Biology
• Medical Imaging

Background:

• Biomedical simulations often follow a standard image-based geometric modeling and simulation workflow.
• This process involves image processing, geometric model generation, property assignment, numerical simulation, and result visualization.

Purpose of the Study:

• To provide an overview of software systems for implementing image-based geometric modeling and simulation workflows.
• To describe both highly integrated environments and loosely integrated pipelines for these processes.
• To present applications of these pipelines in translational biomedical research, specifically in electrophysiology.

Main Methods:

• Review and categorization of existing software systems for biomedical simulation pipelines.
• Description of highly integrated problem-solving environments.
• Explanation of loosely integrated pipelines, emphasizing independent program function and file-based communication with scripting for automation.

Main Results:

• Identification of two main approaches for implementing simulation sequences: integrated environments and loosely integrated pipelines.
• Demonstration of the utility of loosely integrated pipelines through three specific applications in translational biomedical research.
• Highlighting the flexibility and automation capabilities of loosely integrated pipelines.

Conclusions:

• Loosely integrated pipelines offer a flexible and automatable approach for image-based geometric modeling and simulation in biomedicine.
• These pipelines are valuable tools for advancing translational research, particularly in fields like electrophysiology.
• The presented overview aids researchers in selecting and implementing appropriate software systems for their simulation needs.