Computer-aided pulmonary image analysis in small animal models

Ziyue Xu, Ulas Bagci*, Awais Mansoor, Gabriela Kramer-Marek, Brian Luna, Andre Kubler, Bappaditya Dey, Brent Foster, Georgios Z. Papadakis, Jeremy V. Camp, Colleen B. Jonsson, William R. Bishai, Sanjay Jain, Jayaram K. Udupa, Daniel J. Mollura

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


Purpose: To develop an automated pulmonary image analysis framework for infectious lung diseases in small animal models. Methods: The authors describe a novel pathological lung and airway segmentation method for small animals. The proposed framework includes identification of abnormal imaging patterns pertaining to infectious lung diseases. First, the authors system estimates an expected lung volume by utilizing a regression function between total lung capacity and approximated rib cage volume. A significant difference between the expected lung volume and the initial lung segmentation indicates the presence of severe pathology, and invokes a machine learning based abnormal imaging pattern detection system next. The final stage of the proposed framework is the automatic extraction of airway tree for which new affinity relationships within the fuzzy connectedness image segmentation framework are proposed by combining Hessian and gray-scale morphological reconstruction filters. Results: 133 CT scans were collected from four different studies encompassing a wide spectrum of pulmonary abnormalities pertaining to two commonly used small animal models (ferret and rabbit). Sensitivity and specificity were greater than 90% for pathological lung segmentation (average dice similarity coefficient > 0.9). While qualitative visual assessments of airway tree extraction were performed by the participating expert radiologists, for quantitative evaluation the authors validated the proposed airway extraction method by using publicly available EXACT09 data set. Conclusions: The authors developed a comprehensive computer-aided pulmonary image analysis framework for preclinical research applications. The proposed framework consists of automatic pathological lung segmentation and accurate airway tree extraction. The framework has high sensitivity and specificity; therefore, it can contribute advances in preclinical research in pulmonary diseases.

Original languageEnglish (US)
Pages (from-to)3896-3910
Number of pages15
JournalMedical Physics
Issue number7
StatePublished - Jul 1 2015
Externally publishedYes


  • CT
  • airway lumen segmentation
  • fuzzy connectedness
  • lung segmentation
  • machine learning
  • small animal model

ASJC Scopus subject areas

  • Biophysics
  • Radiology Nuclear Medicine and imaging


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