pkhpc1pyr 0.0.4

Scripts and functions for the pharmacokinetic modeling of hyperpolarized [1-13C]-pyruvate.

HP C1-Pyruvate Pharmacokinetic Modeling Package for Python

Purpose

This package was meant to create a more user friendly, open source version of the MATLAB developed by the MD Anderson Magnetic Resonance Engineering Laboratory. The original repository is available at https://github.com/mda-mrsl/HP-C1Pyr-PK

These scripts calculate the relationship between [1-13C]-pyruvate and [1-13C]-lactate, but can easily be extended to include other metabolites.

There are three base models, of differing complexity, which include a different number of physical compartments:

The scripts titled P2L3*.py describe signal evolution between two chemical pools and three physical compartments. The three-compartment model is the most physiologically accurate among these models, but it is also the most computationally intensive, requiring the largest number of descriptive parameters.

The scripts titled P2L2*.py are for the PK model with two chemical pools and two physical compartments. Here, HP pyruvate and lactate in the extravascular/extracellular space is assumed to be very well mixed with HP pyruvate in the intracellular space - and separate from pyr/lac in the vascular supply.

The scripts titled P2L1*.py represent a simple precursor-product model, which does not consider physical compartmentalization of imaging agents. Equivalently, this assumes that all compartments (vascular; extravascular/extracellular; and cellular) are well mixed.

Each script is accompanied by utilities and a test function which runs a model and plots the results for given parameters.

Installation

Running requires python version 3.10 or compatible

Can be installed from Pypi repository with pip
pip install pkhpc1pyr
The required dependencies can be found in the file requirements.txt and installed with the command
pip install -r requirements.txt

The installation can be tested by calling the TestP2L* functions without any arguments. For example:
import pkhpc1pyr as pk
pk.tests.TestP2L3()

Contact

For questions about code or maintenance please contact Ryan Boyce
[e-mail]
For further questions about the original MATLAB repository please contact Dr. Jim Bankson
[e-mail]