3D Microanatomical Atlasing

Whole-organism phenotyping is vital for understanding how genetic and environmental factors determine normal and disease phenotypes. Atlas resources that integrate unbiased “-omics” and tissue morphology facilitate this goal.

While traditional 2D histology provides subcellular detail, its inherent limitations — destructive preparation, two-dimensional perspective, and sampling artifacts — restrict insights into the 3D structure and organization of cells within tissues.

To overcome these limitations, we integrate microCT imaging to add 3D representations of cells and organs, allowing researchers to interrogate spatial relationships between structures and explore microanatomy in virtual environments. MicroCT images serve an integrative role, anchoring histology, fluorescence and ultrastructural imaging, and large-scale “-omic” data across length scales.

We have imaged Daphnia, zebrafish, and Drosophila at an unprecedented combination of 5 mm field-of-view (FOV) with 0.5 μm isotropic resolution at Lawrence Berkeley National Laboratory. Data are presented using the 4-planar viewer (sagittal, transverse, coronal and 3D) via Neuroglancer, with organ segmentation and 3D visualization capabilities.

By incorporating molecular and morphological data within a unified, organism-wide context, this 3D atlas platform enables multi-scale interrogation of how genetic variation and environmental perturbations drive phenotype — serving as a foundation for future applications across model organisms and human atlases.