# Allen Brain Cell (ABC) Atlas **URL:** https://community.brain-map.org/c/how-to/abc-atlas/19.md?page=1 [Latest](https://community.brain-map.org/latest.md) · [Categories](https://community.brain-map.org/categories.md) · [Tags](https://community.brain-map.org/tags.md) **Page:** 2 --- ## [New Imputed Gene Data for the Whole Mouse Brain Now Explorable in ABC Atlas](https://community.brain-map.org/t/new-imputed-gene-data-for-the-whole-mouse-brain-now-explorable-in-abc-atlas/3723)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [October 1, 2024, 2:59pm UTC](https://community.brain-map.org/t/new-imputed-gene-data-for-the-whole-mouse-brain-now-explorable-in-abc-atlas/3723 "2024-10-01T14:59:20Z")
The ABC Atlas has been updated with new data! This update adds the MERFISH imputed gene data created in Yao et al., adding more than 8,000 genes to the MERFISH dataset. From the 10x scRNAseq whole brain data, additiona… --- ## [Correspondence of anatomical divisions in MERFISH and scRNA-seq data](https://community.brain-map.org/t/correspondence-of-anatomical-divisions-in-merfish-and-scrna-seq-data/3592)
**Author:** [@mukamel-lab](https://community.brain-map.org/u/mukamel-lab)\ **Replies:** 1\ **Last updated:** [August 22, 2024, 3:29pm UTC](https://community.brain-map.org/t/correspondence-of-anatomical-divisions-in-merfish-and-scrna-seq-data/3592 "2024-08-22T15:29:55Z")
Thanks for these amazing datasets and tools! I have a question about the relationship between the anatomical division annotations in the spatial transcriptomics (MERFISH) and scRNA-seq data. I was looking at the gene Db… --- ## [Mouse ABC with CCF Coordinates](https://community.brain-map.org/t/mouse-abc-with-ccf-coordinates/3395)
**Author:** [@weiyouzi321](https://community.brain-map.org/u/weiyouzi321)\ **Replies:** 2\ **Last updated:** [August 21, 2024, 12:58pm UTC](https://community.brain-map.org/t/mouse-abc-with-ccf-coordinates/3395 "2024-08-21T12:58:02Z")
ABC project is a great work for the field.Recently i’m trying to integrate mouse ABC with MRI through CCF coordinates.MRI image has been registered to 100um CCF template and I notice ABC CCF Coordinates have also been re… --- ## [ABC Atlas Update Notes - August 20, 2024](https://community.brain-map.org/t/abc-atlas-update-notes-august-20-2024/3588)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [August 20, 2024, 5:33pm UTC](https://community.brain-map.org/t/abc-atlas-update-notes-august-20-2024/3588 "2024-08-20T17:33:49Z")
The ABC Atlas has been updated with new features and improvements! Numeric Features The ABC Atlas can now display continuous values for certain features. Our first numeric feature is the SEA-AD Continuous Pseudo Progre… --- ## [ABC Atlas Update Notes - July 23, 2024](https://community.brain-map.org/t/abc-atlas-update-notes-july-23-2024/3523)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [July 24, 2024, 2:14pm UTC](https://community.brain-map.org/t/abc-atlas-update-notes-july-23-2024/3523 "2024-07-24T14:14:45Z")
The ABC Atlas has been updated with new features and improvements! Hover Syncing Across Data Sets With this release we introduce “hover sync,” a new feature that allows you to quickly see and compare cell property valu… --- ## [Neuromodulator-releasing subclasses UMAP from Yao et. al. 2023](https://community.brain-map.org/t/neuromodulator-releasing-subclasses-umap-from-yao-et-al-2023/3437)
**Author:** [@alwaysnow](https://community.brain-map.org/u/alwaysnow)\ **Replies:** 1\ **Last updated:** [July 17, 2024, 11:25pm UTC](https://community.brain-map.org/t/neuromodulator-releasing-subclasses-umap-from-yao-et-al-2023/3437 "2024-07-17T23:25:59Z")
Hello, I was wondering if the UMAP from figure 3 of Yao et. al. 2023 is planned for incorporation into the ABC Atlas. I noticed that most other UMAPs from the paper have been added, just curious if the modulatory-neurot… --- ## [How to map parcellation indices to anatomical ontology IDs in CCFv3 between the Allen Cell Atlas and Gene Expression Atlases?](https://community.brain-map.org/t/how-to-map-parcellation-indices-to-anatomical-ontology-ids-in-ccfv3-between-the-allen-cell-atlas-and-gene-expression-atlases/3481)
**Author:** [@MBF2313](https://community.brain-map.org/u/MBF2313)\ **Replies:** 0\ **Last updated:** [July 15, 2024, 5:06pm UTC](https://community.brain-map.org/t/how-to-map-parcellation-indices-to-anatomical-ontology-ids-in-ccfv3-between-the-allen-cell-atlas-and-gene-expression-atlases/3481 "2024-07-15T17:06:24Z")
I recently started exploring the Allen Brain Cell Atlas for the adult mouse brain and have been following the guides containing Python examples demonstrating how to access the data. At the same time, I’m using gene expr… --- ## [How MERFISH obtained x,y,z coordinates of each cell](https://community.brain-map.org/t/how-merfish-obtained-x-y-z-coordinates-of-each-cell/3461)
**Author:** [@csy020406](https://community.brain-map.org/u/csy020406)\ **Replies:** 0\ **Last updated:** [July 9, 2024, 7:06am UTC](https://community.brain-map.org/t/how-merfish-obtained-x-y-z-coordinates-of-each-cell/3461 "2024-07-09T07:06:33Z")
I wonder how MERFISH obtained the x, y, z coordinates of each cell. Is there any document explaining the process in detail? I want to know it because I am trying to find out the coordinates of my cells to compare with th… --- ## [ABC Atlas Update Notes - May 14, 2024](https://community.brain-map.org/t/abc-atlas-update-notes-may-14-2024/3329)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 1\ **Last updated:** [June 26, 2024, 1:12pm UTC](https://community.brain-map.org/t/abc-atlas-update-notes-may-14-2024/3329 "2024-06-26T13:12:50Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new features and improvements! Anatomical Annotations With this release we introduce the ability to view spatial data with anatomical annotations. The first… --- ## [ABC Atlas: Example Use Cases (Whole Human Brain)](https://community.brain-map.org/t/abc-atlas-example-use-cases-whole-human-brain/3204)
**Author:** [@rachel.hostetler](https://community.brain-map.org/u/rachel.hostetler)\ **Replies:** 0\ **Last updated:** [April 1, 2024, 6:03pm UTC](https://community.brain-map.org/t/abc-atlas-example-use-cases-whole-human-brain/3204 "2024-04-01T18:03:22Z")
Interested in using the Allen Brain Cell (ABC) Atlas but don’t know where to start? Check out our step-by-step use cases on the whole human brain data from Siletti et al., 2023: Use Case #1 - Experimental Design “A re… --- ## [ABC Atlas Update Notes - March 26, 2024](https://community.brain-map.org/t/abc-atlas-update-notes-march-26-2024/3187)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 1\ **Last updated:** [March 31, 2024, 5:13am UTC](https://community.brain-map.org/t/abc-atlas-update-notes-march-26-2024/3187 "2024-03-31T05:13:24Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new features and improvements! Click to Filter It’s now easier than ever to add and remove cells from your filtered views Hover the cursor over a cell of i… --- ## [ABC Atlas Update Notes - March 13, 2024](https://community.brain-map.org/t/abc-atlas-update-notes-march-13-2024/3153)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [March 12, 2024, 2:21pm UTC](https://community.brain-map.org/t/abc-atlas-update-notes-march-13-2024/3153 "2024-03-12T14:21:21Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new features and improvements! Slide View Data sets comprised of spatial slices of tissue now offer new viewing options including the ability to scroll throu… --- ## [ABC Atlas Update Notes - February 27, 2024](https://community.brain-map.org/t/abc-atlas-update-notes-february-27-2024/3105)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [February 26, 2024, 3:44pm UTC](https://community.brain-map.org/t/abc-atlas-update-notes-february-27-2024/3105 "2024-02-26T15:44:45Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new features and improvements! Gene Expression Filtering It is now possible to filter views by gene expression value. From the Genes tab, after selecting a g… --- ## [Access to raw (bam or fastq) Smart-seq2 human cortex scRNA-seq](https://community.brain-map.org/t/access-to-raw-bam-or-fastq-smart-seq2-human-cortex-scrna-seq/3102)
**Author:** [@davidaknowles](https://community.brain-map.org/u/davidaknowles)\ **Replies:** 2\ **Last updated:** [February 27, 2024, 12:48am UTC](https://community.brain-map.org/t/access-to-raw-bam-or-fastq-smart-seq2-human-cortex-scrna-seq/3102 "2024-02-27T00:48:33Z")
Hi. My research group is interested in obtaining access to the raw (bam or fastq) Smart-seq2 human cortex scRNA-seq data (Human Multiple Cortical Areas SMART-seq - brain-map.org). This would be with a view to doing alter… --- ## [ABC Atlas User Guide: Visualization Frames](https://community.brain-map.org/t/abc-atlas-user-guide-visualization-frames/2447)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [July 8, 2023, 5:43pm UTC](https://community.brain-map.org/t/abc-atlas-user-guide-visualization-frames/2447 "2023-07-08T17:43:06Z")
Visualization Frame The ABC Atlas allows you to view up to four visualizations at the same time. When viewing multiple visualizations, the active frame is indicated by a bold outline. Only the active frame will be affect… --- ## [ABC Atlas User Guide: Tools](https://community.brain-map.org/t/abc-atlas-user-guide-tools/2446)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [July 8, 2023, 5:37pm UTC](https://community.brain-map.org/t/abc-atlas-user-guide-tools/2446 "2023-07-08T17:37:24Z")
Tools Please note, your device, internet connection, browser, and other factors can influence performance and loading speed. For best results, we recommend using the ABC Atlas in an updated version of the Chrome browser … --- ## [Update Notes - February 13, 2024](https://community.brain-map.org/t/update-notes-february-13-2024/3070)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [February 9, 2024, 3:28pm UTC](https://community.brain-map.org/t/update-notes-february-13-2024/3070 "2024-02-09T15:28:52Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new features and improvements! Zoom & Pan View Syncing Comparing features across views is now even easier. Zoom & Pan Syncing creates spatial sync groups bet… --- ## [Full name for cell taxa](https://community.brain-map.org/t/full-name-for-cell-taxa/2936)
**Author:** [@ohmstead](https://community.brain-map.org/u/ohmstead)\ **Replies:** 0\ **Last updated:** [January 18, 2024, 8:49pm UTC](https://community.brain-map.org/t/full-name-for-cell-taxa/2936 "2024-01-18T20:49:31Z")
Is there a table with full names for abbreviated cluters/supertypes/subclasses/classes in the WMB atlas? I know the flagship papers have many of these abbreviations, but for a subclass like “015 ENTmv-PA-COAp Glut,” it c… --- ## [\# cells per cluster](https://community.brain-map.org/t/cells-per-cluster/2888)
**Author:** [@susant](https://community.brain-map.org/u/susant)\ **Replies:** 2\ **Last updated:** [January 16, 2024, 11:41pm UTC](https://community.brain-map.org/t/cells-per-cluster/2888 "2024-01-16T23:41:04Z")
trying to estimate the relative prevalence of particular cell types (clusters) in a given brain region. I have downloaded the cluster ID’s and can look them up in Supplemental Table 7 in Yao (or cl.df.CCN202307220). Woul… --- ## [Analyze striatal 10x data by Seurat in R](https://community.brain-map.org/t/analyze-striatal-10x-data-by-seurat-in-r/2899)
**Author:** [@lingwu217](https://community.brain-map.org/u/lingwu217)\ **Replies:** 1\ **Last updated:** [January 16, 2024, 5:58pm UTC](https://community.brain-map.org/t/analyze-striatal-10x-data-by-seurat-in-r/2899 "2024-01-16T17:58:50Z")
Hi thanks for the incredible resource! I am a single cell beginner and was trying to find the 10x v3 data that’s disected from striatum and analyze in R by Seurat. Could you help to locate the files? Does the matrix f… --- ## [Update Notes - December 12, 2023](https://community.brain-map.org/t/update-notes-december-12-2023/2775)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [December 11, 2023, 11:05pm UTC](https://community.brain-map.org/t/update-notes-december-12-2023/2775 "2023-12-11T23:05:51Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new features and improvements! Overview The new icon panel on the left allows quick navigation between Control Panel tabs. The filters and settings on each t… --- ## [Update Notes - November 7, 2023](https://community.brain-map.org/t/update-notes-november-7-2023/2696)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [November 7, 2023, 6:09pm UTC](https://community.brain-map.org/t/update-notes-november-7-2023/2696 "2023-11-07T18:09:00Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new data, features and improvements! New Data Seattle Alzheimer’s Disease Brain Cell Atlas The Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) is a con… --- ## [Update Notes - October 17, 2023](https://community.brain-map.org/t/update-notes-october-17-2023/2650)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [October 18, 2023, 1:48pm UTC](https://community.brain-map.org/t/update-notes-october-17-2023/2650 "2023-10-18T13:48:08Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new features and performance improvements! New “About” tab in the Control Panel It is now easier than ever to find descriptions and downloads for the data in… --- ## [Update Notes - Sept 12, 2023](https://community.brain-map.org/t/update-notes-sept-12-2023/2587)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [September 12, 2023, 2:05pm UTC](https://community.brain-map.org/t/update-notes-sept-12-2023/2587 "2023-09-12T14:05:31Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new data, features and improvements! New Data We are pleased to bring you updated whole-mouse-brain data with improvements to the cell types taxonomy. This c… --- ## [ABC Atlas: August Update Notes](https://community.brain-map.org/t/abc-atlas-august-update-notes/2549)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [August 21, 2023, 4:07pm UTC](https://community.brain-map.org/t/abc-atlas-august-update-notes/2549 "2023-08-21T16:07:15Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new features and improvements! Frame cloning Now, when adding frames using the change layout tool, new frames will start as copies of the selected frame, pre… --- ## [ABC Atlas User Guide: Navigation Modes](https://community.brain-map.org/t/abc-atlas-user-guide-navigation-modes/2448)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [July 8, 2023, 5:47pm UTC](https://community.brain-map.org/t/abc-atlas-user-guide-navigation-modes/2448 "2023-07-08T17:47:39Z")
Navigation modes ABC Atlas allows two navigation modes, Zoom & Pan or Cell Selection. The active navigation mode is indicated by and can be changed using the icons in the top right of the active frame. Only one navigati… --- ## [ABC Atlas User Guide: Mouse Whole-Brain Transcriptomic Cell Type Atlas Data and Dimensions](https://community.brain-map.org/t/abc-atlas-user-guide-mouse-whole-brain-transcriptomic-cell-type-atlas-data-and-dimensions/2445)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 3\ **Last updated:** [July 18, 2023, 3:00pm UTC](https://community.brain-map.org/t/abc-atlas-user-guide-mouse-whole-brain-transcriptomic-cell-type-atlas-data-and-dimensions/2445 "2023-07-18T15:00:47Z")
Mouse Whole-Brain Transcriptomic Cell Type Atlas - Data & Dimensions For more detail and to download full datasets see the Project Page or GitHub for an overview of all the data including notebooks with examples. Comm… [Previous page](https://community.brain-map.org/c/how-to/abc-atlas/19.md)