HuDSeN atlas and spatial gene expression database

HuDSeN atlas and spatial gene expression database integrates digital 3D models of the human embryonic brain with spatial gene expression datasets and annotated histology sections to enable analysis of spatial–temporal gene expression during Carnegie Stages 12–23 (approximately 26–56 days post-conception).

Key Features:

• Three-Dimensional (3D) Atlas Development: A detailed 3D atlas spanning 12 developmental stages corresponding to Carnegie Stages 12–23 (approximately 26–56 days post-conception) with major subdivisions delineated by anatomical landmarks and gene expression.
• Optical Projection Tomography (OPT): Virtual 3D anatomical models are generated from intact specimens using OPT imaging.
• Gene Expression Mapping: Gene expression data derived from in situ hybridization and immunohistochemistry are mapped onto representative 3D models using MAPAINT software.
• Developmental Neuroanatomic Ontology: Anatomical domains are defined by morphological landmarks and comparative vertebrate expression patterns and are linked to a developmental neuroanatomic ontology.
• Interpolation Software: Interpolation software digitally generates complete anatomical domains from incomplete datasets to fill partial data gaps.
• Gene Expression Database: Hosts spatial gene expression data for approximately 100 genes.
• Annotated Histology Sections: Includes annotated histology sections integrated with 3D models and gene expression mappings.

Scientific Applications:

• Developmental Neurobiology: Identification and refinement of anatomical domain boundaries in the human embryonic brain across Carnegie Stages 12–23.
• Spatial Transcriptomics and Genetics: Analysis of spatial dynamics of gene expression from in situ hybridization and immunohistochemistry for ~100 genes during early human development.
• Comparative and Evolutionary Developmental Biology: Comparative studies across vertebrates by integrating spatial gene expression with morphological domain definitions.
• Histology–Model Correlation: Correlation of annotated histology sections with 3D anatomical models to support anatomical interpretation of gene expression patterns.

Methodology:

Virtual 3D model generation by Optical Projection Tomography (OPT), mapping of in situ hybridization and immunohistochemistry data onto models using MAPAINT, use of interpolation software to complete anatomical domains, and linkage of domains to a developmental neuroanatomic ontology.