AVATREE: An Open-Source Computational Modelling Framework Modelling Anatomically Valid Airway TREE Conformations

PLoS One. 2020 Apr 3;15(4):e0230259. doi: 10.1371/journal.pone.0230259. eCollection 2020.


This paper presents AVATREE, a computational modelling framework that generates Anatomically Valid Airway tree conformations and provides capabilities for simulation of broncho-constriction apparent in obstructive pulmonary conditions. Such conformations are obtained from the personalized 3D geometry generated from computed tomography (CT) data through image segmentation. The patient-specific representation of the bronchial tree structure is extended beyond the visible airway generation depth using a knowledge-based technique built from morphometric studies. Additional functionalities of AVATREE include visualization of spatial probability maps for the airway generations projected on the CT imaging data, and visualization of the airway tree based on local structure properties. Furthermore, the proposed toolbox supports the simulation of broncho-constriction apparent in pulmonary diseases, such as chronic obstructive pulmonary disease (COPD) and asthma. AVATREE is provided as an open-source toolbox in C++ and is supported by a graphical user interface integrating the modelling functionalities. It can be exploited in studies of gas flow, gas mixing, ventilation patterns and particle deposition in the pulmonary system, with the aim to improve clinical decision making.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Asthma / diagnostic imaging
  • Asthma / pathology*
  • Computer Simulation*
  • Humans
  • Imaging, Three-Dimensional*
  • Lung / drug effects
  • Lung / pathology*
  • Models, Anatomic*
  • Pulmonary Disease, Chronic Obstructive / diagnostic imaging
  • Pulmonary Disease, Chronic Obstructive / pathology*
  • Tomography, X-Ray Computed

Grant support

This work has been co‐financed by the European Regional Development Fund of the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH – CREATE - INNOVATE Take-A-Breath, under grant agreement No. T1EDK-03832). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.