Allen Mouse CCF - gallery of tools and publications

A gallery of publications and tools using the Allen Mouse Common Coordinate Framework

Distributed coding of choice, action, and engagement across the mouse brain, Steinmetz et. al. 2019

Mapping Mesoscale Axonal Projections in the Mouse Brain Using A 3D Convolutional Network, Friedmann et. al. 2019

High-throughput mapping of mesoscale connectomes in individual mice, Huang et, al. 2018

Biased connectivity of brain-wide inputs to ventral subiculum output neurons, Wee and MacAskill, 2019

Single-trial neural dynamics are dominated by richly varied movements, Musall et. al. 2019

Visualization and Quantification of Post-stroke Neural Connectivity and Neuroinflammation Using Serial Two-Photon Tomography in the Whole Mouse Brain, Poinsatte et. al. 2019

BrainRender - python library to render 3D anatomical data

Greedy low-rank algorithm for spatial connectome regression, Kürschner et al. 2019

Hierarchical organization of cortical and thalamic connectivity, Harris et. al. 2019

Enhanced and unified anatomical labeling for a common mouse brain atlas. Chon et. al. 2019

Sensory and Behavioral Components of Neocortical Signal Flow in Discrimination Tasks with Short-term Memory. Gallero-Salas et. al. 2020

CellFinder: fully automated 3D cell detection and registration of whole-brain images.

Machine learning analysis of whole mouse brain vasculature. Todorov et al. 2020

Spatiotemporal refinement of signal flow through association cortex during learning. Gilad & Helmchen, 2020

Got a tool or publication you want to share? What other examples are out there? Join in the conversation below!


cocoframer: Functions for the Allen Institute’s Mouse Common Coordinate Framework (CCF) in R.

A platform for brain-wide functional ultrasound imaging and analysis of circuit dynamics in behaving mice. Brunner et al 2020

A perceptual decision requires sensory but not action coding in mouse cortex. Zatka-Haas 2020

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