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‎README.md‎

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# Allen Brain Cell Atlas - Data Access
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The Allen Brain Cell Atlas (ABC Atlas) aims to empower researchers worldwide to explore and analyze multiple whole-brain datasets simultaneously. As the Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas, this groundbreaking platform will keep growing, opening up endless possibilities for groundbreaking discoveries and breakthroughs in neuroscience. With the ABC Atlas, researchers everywhere can gain new insights into the brain’s complex workings, advancing our understanding of this amazing organ in ways we never thought possible.
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The Allen Brain Cell Atlas (ABC Atlas) aims to empower researchers worldwide to
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explore and analyze multiple whole-brain datasets simultaneously. As the Allen
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Institute and its collaborators continue to add new modalities, species, and
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insights to the ABC Atlas, this groundbreaking platform will keep growing,
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opening up endless possibilities for groundbreaking discoveries and
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breakthroughs in neuroscience. With the ABC Atlas, researchers everywhere can
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gain new insights into the brain’s complex workings, advancing our
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understanding of this amazing organ in ways we never thought possible.
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## ABC Atlas Data Access JupyterBook
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## ABC Atlas Data Access JupyterBook Website
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https://AllenInstitute.github.io/abc_atlas_access
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## How to contribute
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[JupyterBook Contribution Guide](docs/jupyterbook/README.md)
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Note: for scientific questions regarding the data this repository is accessing,
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please use the
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[Allen Institute's community forum](https://community.brain-map.org/).
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If you are having an issue with the code or notebooks not running properly
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please open an issue on this Github respoitory. However, please see below.
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## Level of support
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We are not currently supporting this code, but simply releasing it to the community AS IS but are not able to provide any guarantees of support. The community is welcome to submit issues, but you should not expect an active response.
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We are not currently supporting this code, but simply releasing it to the
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community AS IS but are not able to provide any guarantees of support. The
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community is welcome to submit issues, but you should not expect an active
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response.

‎_config.yml‎

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author: Allen Institute
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copyright: "2023"
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logo: ./images/allen_logo.jpeg
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exclude_patterns: [_build, .DS_Store] # Patterns to skip when building the book.
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exclude_patterns: [_build, .DS_Store, .pytest_cache, tests, "**.ipynb_checkpoints"] # Patterns to skip when building the book.
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only_build_toc_files: true # Auto-exclude files not in the toc
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bibtex_bibfiles:
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- references.bib

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‎_static/WHB-taxonomy/20240330/cluster.html‎

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‎_static/WHB-taxonomy/20240330/neurotransmitter.html‎

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<html>
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<head><title>WHB-taxonmy: neurotransmitter types</title></head>
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<link rel="stylesheet" type="text/css" href="../../simple_style.css"/>
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<body>
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<table border="1" class="dataframe mystyle">
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<thead>
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<tr style="text-align: right;">
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<th>neurotransmitter</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td><div id="CS202210140_3821"></div><div class="circle" style="background-color:#22A5BB"></div><div class="celltext">VGLUT1 VGLUT2</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3824"></div><div class="circle" style="background-color:#2252C2"></div><div class="celltext">VGLUT2 VGLUT3</div></td>
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</tr>
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<tr>
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<td><div id="nan"></div><div class="circle" style="background-color:#ebebeb"></div><div class="celltext">Other</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3814"></div><div class="circle" style="background-color:#95369C"></div><div class="celltext">GABA VGLUT3</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3810"></div><div class="circle" style="background-color:#FF3358"></div><div class="celltext">GABA</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3815"></div><div class="circle" style="background-color:#6B0C48"></div><div class="celltext">GLY</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3820"></div><div class="circle" style="background-color:#2BDFD1"></div><div class="celltext">VGLUT1</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3822"></div><div class="circle" style="background-color:#2B93DF"></div><div class="celltext">VGLUT1 VGLUT2 VGLUT3</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3823"></div><div class="circle" style="background-color:#196AA5"></div><div class="celltext">VGLUT2</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3818"></div><div class="circle" style="background-color:#8C7063"></div><div class="celltext">HDC VGLUT2</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3807"></div><div class="circle" style="background-color:#4FE3AB"></div><div class="celltext">CHOL VGLUT1 VGLUT2</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3816"></div><div class="circle" style="background-color:#423B77"></div><div class="celltext">GLY VGLUT2</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3813"></div><div class="circle" style="background-color:#8C4F7F"></div><div class="celltext">GABA VGLUT2</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3809"></div><div class="circle" style="background-color:#8BAD78"></div><div class="celltext">DA VGLUT2</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3825"></div><div class="circle" style="background-color:#2B39DF"></div><div class="celltext">VGLUT3</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3819"></div><div class="circle" style="background-color:#3F38B8"></div><div class="celltext">SER VGLUT3</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3808"></div><div class="circle" style="background-color:#4F90B2"></div><div class="celltext">CHOL VGLUT3</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3812"></div><div class="circle" style="background-color:#C6525E"></div><div class="celltext">GABA HDC VGLUT2</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3811"></div><div class="circle" style="background-color:#FF553D"></div><div class="celltext">GABA HDC</div></td>
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</tr>
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<tr>
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<td><div id="CS202210140_3817"></div><div class="circle" style="background-color:#FF7621"></div><div class="celltext">HDC</div></td>
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</tr>
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</tbody>
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</table>
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</body>
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</html>.
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