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

Abstract

Background Immunofluorescent 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. Results We 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) program Conclusion We 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.

LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung

“…The NIH LungMAP consortium was created to centralize the creation of standard reference maps that span regions of the lung and peripheral airway from mouse (lifespan) and human (preterm viability through late childhood) development [1]. In its first phase, LungMAP produced a collection of diverse complementary molecular and imaging datasets for mouse and human samples and built a centralized repository of donor samples generously consented for research by family members of deceased infants, children and young adults (BRINDL) [2][3][4]. Now in its second phase, a major focus of the LungMAP consortium is on the harmonization of datasets across lung location, developmental time points, ethnicity and technology.…”