# Allen Mouse CCF - gallery of tools and publications

**URL:** <https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373>\
**Category:** Show & Tell\
**Tags:** atlas-reference-maps\
**Created:** [November 29, 2019, 4:38am UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373 "2019-11-29T04:38:18Z")\
**Posts on this page:** 16\
**Page:** 1

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**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [November 29, 2019, 4:38am UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/1 "2019-11-29T04:38:18Z")

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A gallery of publications and tools using the [Allen Mouse Common Coordinate Framework](https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359)

New! Gallery can also be viewed as a [collection](https://twitter.com/i/events/1371560297589207040?s=20).

> **[Distributed coding of choice, action, and engagement across the mouse brain, Steinmetz et. al. 2019](https://www.nature.com/articles/s41586-019-1787-x)**

> <https://twitter.com/SteinmetzNeuro/status/1199796599834083328>

> [**Mapping Mesoscale Axonal Projections in the Mouse Brain Using A 3D Convolutional Network, Friedmann et. al. 2019**](https://www.biorxiv.org/content/10.1101/812644v1)

> <https://twitter.com/JustusKebschull/status/1186399041317326848>

> [**High-throughput mapping of mesoscale connectomes in individual mice, Huang et, al. 2018**](https://www.biorxiv.org/content/10.1101/422477v1)

> <https://twitter.com/wholebrainsuite/status/1042849186268557312>

> [**Biased connectivity of brain-wide inputs to ventral subiculum output neurons, Wee and MacAskill, 2019**](https://www.biorxiv.org/content/10.1101/726406v1)

> <https://twitter.com/MacAskillAF/status/1186645142377287680>

> [**Single-trial neural dynamics are dominated by richly varied movements, Musall et. al. 2019**](https://www.nature.com/articles/s41593-019-0502-4)

[https://twitter.com/NatureNeuro/status/1179018654215757824](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](https://www.frontiersin.org/articles/10.3389/fnins.2019.01055/full)

> <https://twitter.com/FrontNeurosci/status/1182682149230526464>

> **[BrainRender - python library to render 3D anatomical data](https://github.com/BrancoLab/BrainRender)**

> <https://twitter.com/Federico_claudi/status/1175783638962769922/photo/1>

> [Greedy low-rank algorithm for spatial connectome regression, Kürschner et al. 2019](https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-019-0077-0)

> <https://twitter.com/KameronDHarris/status/1030396975018127361>

> **[Hierarchical organization of cortical and thalamic connectivity, Harris et. al. 2019](https://www.nature.com/articles/s41586-019-1716-z)**

> <https://twitter.com/AllenInstitute/status/1189898714229305344>

> [**Enhanced and unified anatomical labeling for a common mouse brain atlas. Chon et. al. 2019**](https://www.nature.com/articles/s41467-019-13057-w)

> <https://twitter.com/DanVanselow/status/1195012991462313985>

> [**Sensory and Behavioral Components of Neocortical Signal Flow in Discrimination Tasks with Short-term Memory. Gallero-Salas et. al. 2020**](https://www.biorxiv.org/content/10.1101/2020.01.13.904284v1)

> <https://twitter.com/FritjofHelmchen/status/1217462044775063552>

> [**CellFinder: fully automated 3D cell detection and registration of whole-brain images.**](https://github.com/SainsburyWellcomeCentre/cellfinder)

[https://twitter.com/adamltyson/status/1229785595834257408](https://twitter.com/adamltyson/status/1229785595834257408)

> **[Machine learning analysis of whole mouse brain vasculature. Todorov et al. 2020](https://www.nature.com/articles/s41592-020-0792-1)**

[https://twitter.com/erturklab/status/1247626310563880960](https://twitter.com/erturklab/status/1247626310563880960)

> **[Spatiotemporal refinement of signal flow through association cortex during learning. Gilad & Helmchen, 2020](http://rdcu.be/b3sYb)**

[https://twitter.com/FritjofHelmchen/status/1247840034205708294](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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**Author:** ![lucasg](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lucasg/32/35_2.png) [@lucasg](https://community.brain-map.org/u/lucasg)\
**Post date:** [December 5, 2019, 7:18pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/2 "2019-12-05T19:18:37Z")

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> **[cocoframer: Functions for the Allen Institute’s Mouse Common Coordinate Framework (CCF) in R.](https://github.com/alleninstitute/cocoframer)**

[https://twitter.com/hypercompetent/status/1128721246063972352](https://twitter.com/hypercompetent/status/1128721246063972352)

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**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [April 14, 2020, 10:36pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/3 "2020-04-14T22:36:05Z")

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> [**A platform for brain-wide functional ultrasound imaging and analysis of circuit dynamics in behaving mice. Brunner et al 2020**](https://www.biorxiv.org/content/10.1101/2020.04.10.035436v2)

> <https://twitter.com/Gozzi_Ale/status/1250036165987766272?s=20>

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**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [April 14, 2020, 10:38pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/4 "2020-04-14T22:38:30Z")

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> [**A perceptual decision requires sensory but not action coding in mouse cortex. Zatka-Haas et.al. 2020**](https://www.biorxiv.org/content/10.1101/501627v3)

[https://twitter.com/peterzh/status/1249261413291503621](https://twitter.com/peterzh/status/1249261413291503621)

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**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [October 18, 2020, 6:28pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/5 "2020-10-18T18:28:09Z")

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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)**](https://www.ucl.ac.uk/neuropixels/training/2020-neuropixels-course)

[![](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/2c36b8de45526a669d63a6840c80425a47a6de78.jpeg "2020 Lecture 3.07 - Reconstructing Neuropixels tracks 2D anatomy - Andrew Peters (UCL)") ](https://www.youtube.com/watch?v=XX7ZJ_lxt6o)

> [**Video: Reconstructing Neuropixels tracks from 3D anatomy - Steven Wes (IBL)**](https://www.ucl.ac.uk/neuropixels/training/2020-neuropixels-course)

[![](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/625ae0fc585d84ac2726d216ab8b408660650252.jpeg "2020 Lecture 3.08 - Reconstructing Neuropixels tracks from 3D anatomy - Steven West (IBL)") ](https://www.youtube.com/watch?v=q41Fmm0tsfQ)

> [**Video: Aligning Neuropixels tracks to a brain atlas - Mayo Faulkner (IBL)**](https://www.ucl.ac.uk/neuropixels/training/2020-neuropixels-course)

[![](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/fb15c56204cff6b541ce65777f0df0c0bf228d39.jpeg "2020 Lecture 3.09 - Aligning Neuropixels tracks to a brain atlas - Mayo Faulkner (IBL)") ](https://www.youtube.com/watch?v=JWzj_vZYr-g)

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<div class="post-metadata">

**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [March 3, 2021, 10:46pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/6 "2021-03-03T22:46:08Z")

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> [Striatal activity topographically reflects cortical activity. Peters et al, 2021](https://www.nature.com/articles/s41586-020-03166-8)

> <https://twitter.com/flickerfusion/status/1351924316280135682>

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**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [March 15, 2021, 8:25pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/7 "2021-03-15T20:25:46Z")

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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](https://doi.org/10.1016/j.neuron.2020.09.020)

> <https://twitter.com/opto_brain_imag/status/1338096244099592193>

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**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [March 15, 2021, 8:27pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/8 "2021-03-15T20:27:30Z")

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> [Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI, Goubran et al, 2019](https://doi.org/10.1038/s41467-019-13374-0)

[https://twitter.com/NeuroSchnell/status/1201822162551791617](https://twitter.com/NeuroSchnell/status/1201822162551791617)

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<div class="post-metadata">

**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [March 15, 2021, 8:29pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/9 "2021-03-15T20:29:18Z")

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> [Brain mapping across 16 autism mouse models reveals a spectrum of functional connectivity subtypes. Zerbi et al, 2020](https://doi.org/10.1101/2020.10.15.340588)

> <https://twitter.com/Gozzi_Ale/status/1317038833247129601>

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<div class="post-metadata">

**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [March 15, 2021, 8:32pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/10 "2021-03-15T20:32:44Z")

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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://doi.org/10.1101/2021.02.21.432164)

[https://twitter.com/zamakany/status/1364063109518868481](https://twitter.com/zamakany/status/1364063109518868481)

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<div class="post-metadata">

**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [March 16, 2021, 6:06pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/11 "2021-03-16T18:06:30Z")

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> [Molecular atlas of the adult mouse brain. Ortiz et al, 2020](https://advances.sciencemag.org/content/6/26/eabb3446.full)

[https://twitter.com/alfonslopeztena/status/1276800303258497029](https://twitter.com/alfonslopeztena/status/1276800303258497029)

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<div class="post-metadata">

**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [March 16, 2021, 6:07pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/12 "2021-03-16T18:07:46Z")

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> [EBRAIN Brain Atlases](https://ebrains.eu/services/atlases/)

[https://twitter.com/EBRAINS\_eu/status/1341307493436157952](https://twitter.com/EBRAINS_eu/status/1341307493436157952)

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<div class="post-metadata">

**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [March 16, 2021, 6:08pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/13 "2021-03-16T18:08:44Z")

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> [Blue Brain Cell Atlas](https://www.epfl.ch/research/domains/bluebrain/)

> <https://twitter.com/BlueBrainPjt/status/1067728681936842753>

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<div class="post-metadata">

**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [March 30, 2021, 10:15pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/14 "2021-03-30T22:15:43Z")

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> [Cerebral cortical folding, parcellation, and connectivity in humans, nonhuman primates, and mice. Van Essen et al, 2019](https://doi.org/10.1073/pnas.1902299116)

> <https://twitter.com/INM7_ISN/status/1216687208549273600>

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<div class="post-metadata">

**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [April 19, 2021, 4:51pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/15 "2021-04-19T16:51:05Z")

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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](https://www.cell.com/neuron/fulltext/S0896-6273(21)00202-6)

> <https://twitter.com/mlab_cbs/status/1384155839481606146>

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**Author:** ![NicoKiaru](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/nicokiaru/32/285_2.png) [@NicoKiaru](https://community.brain-map.org/u/NicoKiaru)\
**Post date:** [August 15, 2021, 6:34pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-gallery-of-tools-and-publications/373/17 "2021-08-15T18:34:17Z")

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Hello Everybody,

I’d like to share [ABBA](https://biop.github.io/ijp-imagetoatlas/), 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.