Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images

BMC Bioinformatics

Lina Yang¹  Cliburn Chan¹  Scott White¹  Anna Maria Masci¹  Susan E. Wert²  Ravi S. Misra³  Bruce Aronow⁴  Carol B. Hill⁵  Ben Neely⁶  Maryanne Ardini-Polaske⁷  Nathan Gaddis⁷  Scott M. Palmer⁸ 

[1] Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA;Department of Pediatrics Perinatal Institute Divisions of Neonatology, Perinatal and Pulmonary Biology Cincinnati Children’s Hospital Medical Center/Research Foundation, University of Cincinnati College of Medicine, Cincinnati, OH, USA;Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA;Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA;Duke Clinical Research Institute, Duke School of Medicine, Durham, NC, USA;Duke Crucible, Duke University, Durham, NC, USA;RTI International, Research Triangle Park, NC, USA;Vice Chair for Research, Department of Medicine, Director, Respiratory Research, Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA;

关键词: Ontology;    Algorithms;    Biology;    Image processing;    Machine learning;    Image analysis;   

DOI  :  10.1186/s12859-021-04008-8

来源: Springer

【 摘 要 】

BackgroundImmunofluorescent confocal microscopy uses labeled antibodies as probes against specific macromolecules to discriminate between multiple cell types. For images of the developmental mouse lung, these cells are themselves organized into densely packed higher-level anatomical structures. These types of images can be challenging to segment automatically for several reasons, including the relevance of biomedical context, dependence on the specific set of probes used, prohibitive cost of generating labeled training data, as well as the complexity and dense packing of anatomical structures in the image. The use of an application ontology helps surmount these challenges by combining image data with its metadata to provide a meaningful biological context, modeled after how a human expert would make use of contextual information to identify histological structures, that constrains and simplifies the process of segmentation and object identification.ResultsWe propose an innovative approach for the semi-supervised analysis of complex and densely packed anatomical structures from immunofluorescent images that utilizes an application ontology to provide a simplified context for image segmentation and object identification. We describe how the logical organization of biological facts in the form of an ontology can provide useful constraints that facilitate automatic processing of complex images. We demonstrate the results of ontology-guided segmentation and object identification in mouse developmental lung images from the Bioinformatics REsource ATlas for the Healthy lung database of the Molecular Atlas of Lung Development (LungMAP1) programConclusionWe describe a novel ontology-guided approach to segmentation and classification of complex immunofluorescence images of the developing mouse lung. The ontology is used to automatically generate constraints for each image based on its biomedical context, which facilitates image segmentation and classification.

【 授权许可】

CC BY