# Allen Mouse Brain Atlas **URL:** https://community.brain-map.org/c/how-to/mouse-atlas/22.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) --- ## [Documentation: Allen Mouse Brain Atlas](https://community.brain-map.org/t/documentation-allen-mouse-brain-atlas/2846)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [January 4, 2024, 7:59pm UTC](https://community.brain-map.org/t/documentation-allen-mouse-brain-atlas/2846 "2024-01-04T19:59:35Z")
Documentation: Allen Mouse Brain Atlas Document Description In Situ Hybridization Processes and procedures used to perform ISH Informatics Data Processing Design and implementation of the Informatics Data Pipel… --- ## [How to: Allen Mouse Brain Atlas](https://community.brain-map.org/t/how-to-allen-mouse-brain-atlas/2761)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0
This is the online help for the ALLEN Mouse Brain Atlas web application. The Allen Mouse Brain Atlas is a genome-wide, cellular-resolution atlas of gene expression throughout the adult mouse brain. KEY FEATURES: In sit… --- ## [In Situ Hybridization (ISH) Data](https://community.brain-map.org/t/in-situ-hybridization-ish-data/2762)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 3\ **Last updated:** [August 18, 2025, 9:32pm UTC](https://community.brain-map.org/t/in-situ-hybridization-ish-data/2762 "2025-08-18T21:32:55Z")
Viewing Gene Expression Data Gene Search Viewing Search Results Viewing Gene Expression Data The Allen Mouse Brain Atlas offers the following ways for you to find gene expression data: Use Gene Search to locate genes… --- ## [Anatomic gene expression atlas (agea)](https://community.brain-map.org/t/anatomic-gene-expression-atlas-agea/2763)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [December 8, 2023, 6:44pm UTC](https://community.brain-map.org/t/anatomic-gene-expression-atlas-agea/2763 "2023-12-08T18:44:32Z")
What Is AGEA? The AGEA Viewer What Is AGEA? The Allen Institute has built a data-driven three-dimensional atlas of the adult C57Bl/6J mouse brain based on the ISH gene expression images of the Allen Mouse Brain Atlas. … --- ## [How to: Brain Explorer](https://community.brain-map.org/t/how-to-brain-explorer/2764)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 1\ **Last updated:** [June 2, 2026, 5:08pm UTC](https://community.brain-map.org/t/how-to-brain-explorer/2764 "2026-06-02T17:08:09Z")
Installation Windows Mac Installing Atlases Getting Updates Viewing Gene Expression Image Viewer Expression Thresholds Structure Ontology Viewer Gene List Gene Search Toolbar Advanced Features Troubleshooting W… --- ## [Related Studies to Mouse Brain Atlas](https://community.brain-map.org/t/related-studies-to-mouse-brain-atlas/2765)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [December 8, 2023, 6:50pm UTC](https://community.brain-map.org/t/related-studies-to-mouse-brain-atlas/2765 "2023-12-08T18:50:27Z")
Sleep Study Search Results Mouse Strains Study Search Results Sleep Study The Allen Institute partnered with SRI International to examine the effects of sleep deprivation and sleep state in mice. Approximately 20… --- ## [API for Mouse Brain Atlas](https://community.brain-map.org/t/api-for-mouse-brain-atlas/2766)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [December 8, 2023, 6:58pm UTC](https://community.brain-map.org/t/api-for-mouse-brain-atlas/2766 "2023-12-08T18:58:25Z")
Experimental Overview And Metadata Informatics Data Processing 3-D Reference Models Image Alignment Expression Detection Expression Gridding Structure Unionization Expression Grid Search Service The Allen Mouse Brai… --- ## [Bregma-Lambda Distance in High Resolution Allen Brain Atlas: Mouse Brain](https://community.brain-map.org/t/bregma-lambda-distance-in-high-resolution-allen-brain-atlas-mouse-brain/2980)
**Author:** [@sonali.sriranga](https://community.brain-map.org/u/sonali.sriranga)\ **Replies:** 0\ **Last updated:** [January 26, 2024, 11:20am UTC](https://community.brain-map.org/t/bregma-lambda-distance-in-high-resolution-allen-brain-atlas-mouse-brain/2980 "2024-01-26T11:20:40Z")
Hello, I have been using the Allen High Resolution Mouse Brain Atlas (High Resolution Image Viewer :: Allen Brain Atlas: Mouse Brain) to find coordinates for stereotaxic injections and want to know what the bregma-lamda… --- ## [Map cells to their cell type](https://community.brain-map.org/t/map-cells-to-their-cell-type/3195)
**Author:** [@mossishahi](https://community.brain-map.org/u/mossishahi)\ **Replies:** 4\ **Last updated:** [September 27, 2024, 9:21pm UTC](https://community.brain-map.org/t/map-cells-to-their-cell-type/3195 "2024-09-27T21:21:32Z")
Hi everyone! I have downloaded the \[WMB-10Xv2\] expression matrices and also matched them to their corresponding meta data mathcing by cell barcodes in the obs table of h5ad file and csv file of metadata. The last colum… --- ## [Allen Mouse Brain Atlas: Youtube tutorial](https://community.brain-map.org/t/allen-mouse-brain-atlas-youtube-tutorial/3516)
**Author:** [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Replies:** 0\ **Last updated:** [July 22, 2024, 4:44pm UTC](https://community.brain-map.org/t/allen-mouse-brain-atlas-youtube-tutorial/3516 "2024-07-22T16:44:18Z")
--- ## [Is RPKM information included in the scRNA seq dataset?](https://community.brain-map.org/t/is-rpkm-information-included-in-the-scrna-seq-dataset/3554)
**Author:** [@sophiechenhf](https://community.brain-map.org/u/sophiechenhf)\ **Replies:** 1\ **Last updated:** [August 15, 2024, 3:52pm UTC](https://community.brain-map.org/t/is-rpkm-information-included-in-the-scrna-seq-dataset/3554 "2024-08-15T15:52:23Z")
Hi everyone, I am looking at the recent release of Allen Brain Cell Atlas (AWS S3 Explorer) I am wondering in those .h5ad files, e.g. WMB-10Xv3-STR-raw.h5ad, is the RPKM information included? If yes, how can I load them… --- ## [\[New User\] Mouse ISH Brain Atlas Downloading Data Question](https://community.brain-map.org/t/new-user-mouse-ish-brain-atlas-downloading-data-question/4247)
**Author:** [@jacob\_glia](https://community.brain-map.org/u/jacob_glia)\ **Replies:** 3\ **Last updated:** [August 19, 2025, 7:53pm UTC](https://community.brain-map.org/t/new-user-mouse-ish-brain-atlas-downloading-data-question/4247 "2025-08-19T19:53:53Z")
Hi All, I am new to this forum analyzing data from the Allen Institute, so apologies if this question is tagged wrong or otherwise naïve. On the web portal for the mouse ISH database, my query results (e.g. this one) gi… --- ## [Trouble Download xml file from ISH Differential search results](https://community.brain-map.org/t/trouble-download-xml-file-from-ish-differential-search-results/4646)
**Author:** [@AKAnderson](https://community.brain-map.org/u/AKAnderson)\ **Replies:** 4\ **Last updated:** [August 15, 2025, 5:55pm UTC](https://community.brain-map.org/t/trouble-download-xml-file-from-ish-differential-search-results/4646 "2025-08-15T17:55:51Z")
Hello, I’m having trouble downloading the xml file and converting/importing it into an excel. When I selected the xml link at the bottom of my results page, download it, and load it into excel, there is no data within t… --- ## [Possible Error In Atlas Generation](https://community.brain-map.org/t/possible-error-in-atlas-generation/4703)
**Author:** [@rdaggs27](https://community.brain-map.org/u/rdaggs27)\ **Replies:** 2\ **Last updated:** [September 22, 2025, 7:30pm UTC](https://community.brain-map.org/t/possible-error-in-atlas-generation/4703 "2025-09-22T19:30:37Z")
I have had an issue with masking. Can someone take a look at my slice and its mask and inform me as to what structure im observing and how best to troubleshoot? The mask is warped --- ## [Common coordinate framework version 1](https://community.brain-map.org/t/common-coordinate-framework-version-1/4884)
**Author:** [@PolarBean](https://community.brain-map.org/u/PolarBean)\ **Replies:** 5\ **Last updated:** [April 23, 2026, 3:49pm UTC](https://community.brain-map.org/t/common-coordinate-framework-version-1/4884 "2026-04-23T15:49:09Z")
In the CCFv3 whitepaper (https://community.brain-map.org/uploads/short-url/1iSu6ECUHtPXOCatYIme5nWiUa8.pdf) the CCFv1 is mentioned and shown. Is this file available or archived anywhere. I have searched but haven’t b…