PathBase

PathBase provides a repository of histopathology photomicrographs and macroscopic images from background and mutant strains of laboratory mice to support standardized annotation and computational analysis of mouse phenotypes.

Key Features:

• Image repository: Contains annotated histopathology photomicrographs and macroscopic images depicting lesions from background and mutant strains of laboratory mice.
• MPATH integration: Uses MPATH (mouse pathology ontology) for annotation and coding of images.
• Standardized diagnoses: Employs ontology-based coding to standardize diagnostic terminology across images.
• Computational analysis support: Enables sophisticated data retrieval and computational analysis of mouse phenotypes via coded annotations.
• Phenotype categorization: Facilitates categorization and analysis of pathological findings to link lesions to genetic mutations and phenotypic manifestations.
• Diagnostic and phenotyping support: Supports diagnostic workups and phenotyping of genetically manipulated mice by providing expert-annotated image data.
• Community data sharing: Serves as a community resource for sharing annotated images and pathology expertise among pathologists and researchers.

Scientific Applications:

• Diagnostic workups: Assists diagnostic interpretation of lesions in genetically manipulated mice using annotated images and ontology-based codes.
• Phenotyping of mutant mice: Supports phenotypic characterization of mutant strains by linking histopathological findings to genotypes.
• Ontology-driven analysis: Enables standardized, ontology-driven comparative analysis of pathology across studies and strains.
• Genotype–phenotype studies: Facilitates analysis of how genetic mutations manifest as specific pathological lesions in mice.
• Reproducibility and coding refinement: Aids reproducibility in mouse model studies by promoting consistent coding of mutant mouse phenotypes.

Methodology:

Image annotations and diagnostic coding use MPATH (mouse pathology ontology) to standardize terms and enable data retrieval and computational analysis of mouse phenotypes.