iBrAVE: a unified framework for 3D interactive and integrative analysis of brain atlas data across modalities and scales

Abstract

Understanding the brain requires integrating molecular, structural, and functional information across multiple scales. Despite the rapid expansion of multimodal, multiscale brain atlases in various species, integrative analysis remains challenging. Here, we present iBrAVE, an open-source platform for 3D interactive, integrative analysis of brain atlas datasets across modalities and scales within a common reference space. iBrAVE unifies heterogeneous datasets into five core representations, enabling source-independent analyses from insects to primates. At the single-modality level, it features spatially resolved quantification, as exemplified by single-neuron morphology analyses spanning geometry, topology, projection, clustering, and putative wiring. Across modalities, it links gene expression and neuronal activity with morphologically defined neurons and putative circuits via establishing spatial correspondence. Across scales, it enables bidirectional inference of neuronal identity and synaptic connectivity between light- and electron-microscopy reconstructions via neuronal morphology matching. Thus, iBrAVE provides a unified framework for integrative brain atlas analyses, facilitating data-driven discovery in neuroscience.