Allen Mouse CCF - gallery of tools and publications

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

New! Gallery can also be viewed as a collection.

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

https://twitter.com/NatureNeuro/status/1179018654215757824

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.

https://twitter.com/adamltyson/status/1229785595834257408

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

https://twitter.com/erturklab/status/1247626310563880960

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

https://twitter.com/FritjofHelmchen/status/1247840034205708294

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

2 Likes

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

https://twitter.com/hypercompetent/status/1128721246063972352

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 et.al. 2020

https://twitter.com/peterzh/status/1249261413291503621

1 Like

Videos from the 2020 UCL Neuropixels course showing how to map and compare the electrophysiology data to the CCF

Video: Reconstructing Neuropixels tracks 2D anatomy - Andrew Peters (UCL)

Video: Reconstructing Neuropixels tracks from 3D anatomy - Steven Wes (IBL)

Video: Aligning Neuropixels tracks to a brain atlas - Mayo Faulkner (IBL)

Striatal activity topographically reflects cortical activity. Peters et al, 2021

A Platform for Brain-wide Volumetric Functional Ultrasound Imaging and Analysis of Circuit Dynamics in Awake Mice, Brunner et al, 2020

Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI, Goubran et al, 2019

https://twitter.com/NeuroSchnell/status/1201822162551791617

Brain mapping across 16 autism mouse models reveals a spectrum of functional connectivity subtypes. Zerbi et al, 2020

Volumetric Calcium Imaging of 1 Million Neurons Across Cortical Regions at Cellular Resolution using Light Beads Microscopy. Demas et al, 2021

https://twitter.com/zamakany/status/1364063109518868481

Molecular atlas of the adult mouse brain. Ortiz et al, 2020

https://twitter.com/alfonslopeztena/status/1276800303258497029

EBRAIN Brain Atlases

https://twitter.com/EBRAINS_eu/status/1341307493436157952

1 Like

Blue Brain Cell Atlas

Cerebral cortical folding, parcellation, and connectivity in humans, nonhuman primates, and mice. Van Essen et al, 2019

Fast, cell-resolution, contiguous-wide two-photon imaging to reveal functional network architectures across multi-modal cortical areas. Ota et al, 2021

Hello Everybody,

I’d like to share ABBA, a Fiji plugin that works in conjunction with QuPath. Its aim is to facilitate the registration of serial histology sections to the adult mouse brain atlas.