Semi-automated micro-computed tomography lung segmentation and analysis in mouse models

Jonathan D. Luisi, Jonathan L. Lin, Lorenzo F. Ochoa, Ryan J. McAuley, Madison G. Tanner, Obada Alfarawati, Casey W. Wright, Gracie Vargas, Massoud Motamedi, Bill T. Ameredes

Research output: Contribution to journalArticlepeer-review


Computed Tomography (CT) is a standard clinical tool utilized to diagnose known lung pathologies based on established grading methods. However, for preclinical trials and toxicity investigations in animal models, more comprehensive datasets are typically needed to determine discriminative features between experimental treatments, which oftentimes require analysis of multiple images and their associated differential quantification using manual segmentation methods. Furthermore, for manual segmentation of image data, three or more readers is the gold standard of analysis, but this requirement can be time-consuming and inefficient, depending on variability due to reader bias. In previous papers, microCT image manual segmentation was a valuable tool for assessment of lung pathology in several animal models; however, the manual segmentation approach and the commercial software used was typically a major rate-limiting step. To improve the efficiency, the semi-manual segmentation method was streamlined, and a semi-automated segmentation process was developed to produce: • Quantifiable segmentations: using manual and semi-automated analysis methods for assessing experimental injury and toxicity models, • Deterministic results and efficiency through automation in an unbiased and parameter free process, thereby reducing reader variance, user time, and increases throughput in data analysis, • Cost-Effectiveness: portable with low computational resource demand, based on a cross-platform open-source ImageJ program.

Original languageEnglish (US)
Article number102198
StatePublished - Jan 2023


  • Automated Image Segmentation
  • Bleomycin
  • Image analysis
  • Lung tissue density
  • Manual image segmentation
  • Pulmonary toxicology

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Medical Laboratory Technology


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