Motivation Large-scale neuronal morphologies are essential to neuronal typing, connectivity
characterization and brain modeling. It is widely accepted that automation is critical to the …

Over the last ten years, developments in whole-brain microscopy now allow for high-
resolution imaging of intact brains of small animals such as mice. These complex images …

Abstract 3D brain atlases are key resources to understand the brain's spatial organization
and promote interoperability across different studies. However, unlike the adult mouse brain …

Neurons in the cortex are heterogeneous, sending diverse axonal projections to multiple
brain regions. Unraveling the logic of these projections requires single-neuron resolution …

The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and
archiving neuroimaging data and metadata in a reusable way. First developed for magnetic …

The brain is composed of diverse neuronal and non-neuronal cell types with complex
regional connectivity patterns that create the anatomical infrastructure underlying cognition …

Background Cell clustering is a pivotal aspect of spatial transcriptomics (ST) data analysis
as it forms the foundation for subsequent data mining. Recent advances in spatial domain …

Accurate spatial alignment is essential for any population neuroimaging study, and affine
(12 parameter linear/translation) or rigid (6 parameter rotation/translation) alignments play a …

Recent advances in fluorescence microscopy techniques and tissue clearing, labeling, and
staining provide unprecedented opportunities to investigate brain structure and function …

Advancements in microscopy techniques and computing technologies have enabled
researchers to digitally reconstruct brains at micron scale. As a result, community efforts like …