Allen Mouse CCF - gallery of tools and publications

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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!

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

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

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

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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
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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)

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

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

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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

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

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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

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

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

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EBRAIN Brain Atlases

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

1 Like
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Blue Brain Cell Atlas

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

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

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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.