# 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:** 1\
**Showing post:** 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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