# Allen Mouse Brain Connectivity Atlas **URL:** https://community.brain-map.org/c/how-to/mouse-connectivity-atlas/31.md [Latest](https://community.brain-map.org/latest.md) · [Categories](https://community.brain-map.org/categories.md) · [Tags](https://community.brain-map.org/tags.md) --- ## [Connectivity Atlas: How to](https://community.brain-map.org/t/connectivity-atlas-how-to/3018)
**Author:** [@rachel.hostetler](https://community.brain-map.org/u/rachel.hostetler)\ **Replies:** 0\ **Last updated:** [February 1, 2024, 8:54pm UTC](https://community.brain-map.org/t/connectivity-atlas-how-to/3018 "2024-02-01T20:54:43Z")
This is the online help for the Allen Mouse Connectivity web application. The Allen Mouse Brain Connectivity Atlas is a high-resolution map of neural connections in the mouse brain. Built on an array of transgenic mice … --- ## [Documentation: Mouse Connectivity Atlas](https://community.brain-map.org/t/documentation-mouse-connectivity-atlas/2940)
**Author:** [@LaurenAlfiler](https://community.brain-map.org/u/LaurenAlfiler)\ **Replies:** 0\ **Last updated:** [January 19, 2024, 9:51pm UTC](https://community.brain-map.org/t/documentation-mouse-connectivity-atlas/2940 "2024-01-19T21:51:42Z")
Document Description Overview Technical whitepaper describing the Projection Mapping studies Retinal Projectome Technical whitepaper describing the Retinal Projectome Mapping studies Informatics Data Processi… --- ## [Discrepancies between connectivity data retrieved via API (allenSDK) and the web portal](https://community.brain-map.org/t/discrepancies-between-connectivity-data-retrieved-via-api-allensdk-and-the-web-portal/3766)
**Author:** [@DavideR](https://community.brain-map.org/u/DavideR)\ **Replies:** 1\ **Last updated:** [March 25, 2026, 3:10pm UTC](https://community.brain-map.org/t/discrepancies-between-connectivity-data-retrieved-via-api-allensdk-and-the-web-portal/3766 "2026-03-25T15:10:49Z")
Hi, I’d like to retrieve, via API, the connectivity data for a given target structure, but I had some issues and I don’t know if I’m doing the correct process. The example in the Jupyter notebook “Introduction to the Mo… --- ## [Allen brain connectivity atlast not accessible](https://community.brain-map.org/t/allen-brain-connectivity-atlast-not-accessible/4751)
**Author:** [@martinvinck](https://community.brain-map.org/u/martinvinck)\ **Replies:** 1\ **Last updated:** [November 10, 2025, 8:43pm UTC](https://community.brain-map.org/t/allen-brain-connectivity-atlast-not-accessible/4751 "2025-11-10T20:43:37Z")
hi! It seems the allen brain connectivity atlas is currently offline or not accessible? We are using it for a University course, but on various browsers it seems not to be working since last week Best wishes, Martin --- ## [Difference between data from the AllenSDK and the webpage](https://community.brain-map.org/t/difference-between-data-from-the-allensdk-and-the-webpage/3834)
**Author:** [@DavideR](https://community.brain-map.org/u/DavideR)\ **Replies:** 1\ **Last updated:** [May 19, 2025, 11:49am UTC](https://community.brain-map.org/t/difference-between-data-from-the-allensdk-and-the-webpage/3834 "2025-05-19T11:49:15Z")
I was downloading some connectivity data through the AllenSKD package. I want to have connection data from all the brain structures, projecting to a specific target, so i did: # import libraries and API from allensdk.co… --- ## [Methods for alignment spatial of individual ISI session to cortical surface](https://community.brain-map.org/t/methods-for-alignment-spatial-of-individual-isi-session-to-cortical-surface/3978)
**Author:** [@GreggHeller1](https://community.brain-map.org/u/GreggHeller1)\ **Replies:** 2\ **Last updated:** [December 16, 2024, 4:20pm UTC](https://community.brain-map.org/t/methods-for-alignment-spatial-of-individual-isi-session-to-cortical-surface/3978 "2024-12-16T16:20:15Z")
Hi All, Thank you for this fantastic resource. Its really excellent and will save countless amounts of time, effort and funding. I recently discovered the ability to overlay the ISI imaging sessions in the “Cortical Ma… --- ## [API: Allen Brain Connectivity](https://community.brain-map.org/t/api-allen-brain-connectivity/2988)
**Author:** [@LaurenAlfiler](https://community.brain-map.org/u/LaurenAlfiler)\ **Replies:** 3\ **Last updated:** [September 9, 2024, 12:42pm UTC](https://community.brain-map.org/t/api-allen-brain-connectivity/2988 "2024-09-09T12:42:08Z")
ALLEN BRAIN ATLAS API Experimental Overview and Metadata Informatics Data Processing 3-D Reference Models Image Alignment Projection Data Segmentation Reference-aligned Image Channel Volumes Projection Data Gridding … --- ## [Mouse brain laminar thickness](https://community.brain-map.org/t/mouse-brain-laminar-thickness/3497)
**Author:** [@tmshbr](https://community.brain-map.org/u/tmshbr)\ **Replies:** 0\ **Last updated:** [July 17, 2024, 9:06pm UTC](https://community.brain-map.org/t/mouse-brain-laminar-thickness/3497 "2024-07-17T21:06:01Z")
Hello! I need to calculate the cortical thickness of various areas in the atlas layer by layer. I was wondering if it’s possible to do so in the API currently. Thank you! --- ## [Brain Explorer 3D-Viewer](https://community.brain-map.org/t/brain-explorer-3d-viewer/2986)
**Author:** [@LaurenAlfiler](https://community.brain-map.org/u/LaurenAlfiler)\ **Replies:** 0\ **Last updated:** [January 26, 2024, 11:22pm UTC](https://community.brain-map.org/t/brain-explorer-3d-viewer/2986 "2024-01-26T23:22:22Z")
BRAIN EXPLORER Installation Windows Mac Installing Atlases Getting Updates Viewing Projection Data Image Viewer Structure Ontology Viewer Gene/Projection List Gene Search Toolbar Advanced Features Troubleshooti… --- ## [Reference Data - Mouse Connectivity](https://community.brain-map.org/t/reference-data-mouse-connectivity/2989)
**Author:** [@LaurenAlfiler](https://community.brain-map.org/u/LaurenAlfiler)\ **Replies:** 0\ **Last updated:** [January 27, 2024, 12:08am UTC](https://community.brain-map.org/t/reference-data-mouse-connectivity/2989 "2024-01-27T00:08:25Z")
REFERENCE DATA Viewing the Experiments Keyboard Commands From this tab you can browse from a list of 5 reference dataset experiments. This datasets are also available to add to the cart so you can view them simultan… --- ## [Transgenic Characterization](https://community.brain-map.org/t/transgenic-characterization/2941)
**Author:** [@LaurenAlfiler](https://community.brain-map.org/u/LaurenAlfiler)\ **Replies:** 0\ **Last updated:** [January 19, 2024, 11:59pm UTC](https://community.brain-map.org/t/transgenic-characterization/2941 "2024-01-19T23:59:16Z")
Transgenic Characterization Searching Driver Lines Reporter Lines Retinal Projectome Search Results Experiment Detail Page Using the Zoom And Pan (ZAP) Image Viewer From this tab you can browse and select from repor… --- ## [Projection Dataset](https://community.brain-map.org/t/projection-dataset/2939)
**Author:** [@LaurenAlfiler](https://community.brain-map.org/u/LaurenAlfiler)\ **Replies:** 1\ **Last updated:** [January 26, 2024, 11:42pm UTC](https://community.brain-map.org/t/projection-dataset/2939 "2024-01-26T23:42:41Z")
Searching Source Search Target Search Spatial Search Using the Multiplanar Viewer to Search Experiment Summary View Section Images Viewer Projection Density Image Viewer Correlative Search Cortical Map Viewer Vie…