Repository Overview

Welcome to this GitHub repository, which houses the code corresponding to the article titled "Deciphering Oxygen Distribution and Hypoxia Profiles in the Tumor Microenvironment: A Data-Driven Mechanistic Modeling Approach", DOI: https://doi.org/10.1101/2024.03.04.583326

Key Features

The codebase encompasses a variety of functionalities, including:

• Image processing
• Numerical solution of elliptic Partial Differential Equations (PDE)
• Optimization for parameter estimation
• Validation of the implemented models

Project Structure

Training

The "Training" directory holds scripts responsible for:

# Preprocessing of images
# Solving elliptic PDE numerically
# Optimization for parameter estimation
# Generating plots for the training dataset

Validation

In the "Validation" directory, you will find scripts dedicated to the validation of predictions derived from the modeling framework.

Others

The "Others" directory is equipped with various scripts aimed at generating plots, distinct from those mentioned in the "Training" and "Validation" sections.

Feel free to explore the respective directories to delve into specific aspects of the project. If you have any questions or need further clarification, please don't hesitate to reach out.

Instruction to use

Retrieve the image files for both training and validation from the provided link (https://doi.org/10.5281/zenodo.10796880) in the article, then transfer them to the corresponding subdirectories within the "Image_folder" directory.

Each directory contains a dedicated readme file to facilitate navigation.

Author

Pawan Kumar: @its-Pa1