BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes

Visualizing anatomically registered data with brainrender

(2021) Federico Claudi et al.   eLife

CloudReg: automatic terabyte-scale cross-modal brain volume registration

(2021) Vikram Chandrashekhar et al.   NATURE METHODS

Mesoscale microscopy and image analysis tools for understanding the brain

(2021) Adam L. Tyson et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Homologous organization of cerebellar pathways to sensory, motor, and associative forebrain

(2021) Thomas J. Pisano et al.   Cell Reports

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

(2020) Quanxin Wang et al.   CELL

Mapping mesoscale axonal projections in the mouse brain using a 3D convolutional network

(2020) Drew Friedmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS