# ABC Atlas User Guide: Mouse Whole-Brain Transcriptomic Cell Type Atlas Data and Dimensions **URL:** \ **Category:** Allen Brain Cell (ABC) Atlas\ **Created:** [July 8, 2023, 5:22pm UTC](https://community.brain-map.org/t/abc-atlas-user-guide-mouse-whole-brain-transcriptomic-cell-type-atlas-data-and-dimensions/2445 "2023-07-08T17:22:54Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Elysha-AIBS](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/elysha-aibs/32/828_2.png) [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Post date:** [July 8, 2023, 5:22pm UTC](https://community.brain-map.org/t/abc-atlas-user-guide-mouse-whole-brain-transcriptomic-cell-type-atlas-data-and-dimensions/2445/1 "2023-07-08T17:22:54Z")
## Mouse Whole-Brain Transcriptomic Cell Type Atlas - Data & Dimensions For more detail and to download full datasets see the [Project Page](https://knowledge.brain-map.org/data/LVDBJAW8BI5YSS1QUBG/summary) or [GitHub](https://github.com/AllenInstitute/abc_atlas_access) for an overview of all the data including notebooks with examples. **Common Features** - Gene Expression - Expand the Gene Expression feature to change the selected gene and view the gene expression distribution histogram. - To change genes, click the magnifying glass and enter the name of the gene you wish to see. **Please note, not all genes are included in every dataset.** Click the gene name in the search results to select it and click the droplet icon to apply color to the active frame. - If multiple cell points overlap (e.g. when zoomed out), the highest expression cell will appear “on top” of other cells. This is done to improve visibility of expression patterns. ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/3f28ed256c504f4f6001686c2747f472efc7c977.png) - Cell Types (with 4 layers of subclassification) - Class: The top level of cell type definition in the mouse whole brain taxonomy. It is primarily determined by broad brain region and neurotransmitter type. All cells within a subclass belong to the same class. Class provides a broader categorization of cell types. - Subclass: The coarse level of cell type definition in the mouse whole brain taxonomy. All cells within a supertype belong to the same subclass. Subclass groups together related supertypes. - Supertype: The second finest level of cell type definition in the mouse whole brain taxonomy. All cells within a cluster belong to the same supertype. Supertype groups together similar clusters. - Cluster: The finest level of cell type definition in the mouse whole brain taxonomy. Cells within a cluster share similar characteristics and belong to the same supertype. For a more detailed treatment of cell types explorable in this atlas see: [A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain | Nature](https://www.nature.com/articles/s41586-023-06812-z) **Dataset Visualizations** **MERSCOPE (Spatial slices)** - Gene expression ([500 genes](https://alleninstitute.github.io/abc_atlas_access/gene_lists/MERFISH-C57BL6J-638850/gene_list.html)) - Cell Types (with 4 layers of subclassification) \*Neurotransmitter Type \*Anatomical Division **10x scRNAseq (Whole brain UMAP embedding)** - Gene expression ([32,285 genes](https://alleninstitute.github.io/abc_atlas_access/gene_lists/WMB-10X/gene_list.html)) - Cell Types (with 4 layers of subclassification) - Neurotransmitter type - Dissection Region - Donor ID - Platform - Sex - Genotype See [Introducing the Allen Brain Cell Atlas!](https://community.brain-map.org/t/introducing-the-allen-brain-cell-atlas/2444) for an overview of the tool. Give us your feedback and suggest new features here: [Allen Institute - Feedback](https://docs.google.com/forms/d/e/1FAIpQLSeIaEalEJM-sz4PYMMXNtWvLXdGceqTdfP_Qvp3DIv7uEHSFg/viewform) ---
**Author:** ![MPanday](https://avatars.discourse-cdn.com/v4/letter/m/49beb7/32.png) [@MPanday](https://community.brain-map.org/u/MPanday)\ **Post date:** [July 14, 2023, 3:35pm UTC](https://community.brain-map.org/t/abc-atlas-user-guide-mouse-whole-brain-transcriptomic-cell-type-atlas-data-and-dimensions/2445/2 "2023-07-14T15:35:49Z")
Hi there! This is a really exciting and cool new dataset to explore. Quick question - do you have any information about age/sex/strain of the mice used in the MERSCOPE/MERFISH data? And will there be slices without holes in them? For the 10X scRNAseq, what do the names of the classes represent? Is there a list of that available, or would I be able to find that information in the preprint. Thanks/Merci Beaucoup 🙂 ---
**Author:** ![MPanday](https://avatars.discourse-cdn.com/v4/letter/m/49beb7/32.png) [@MPanday](https://community.brain-map.org/u/MPanday)\ **Post date:** [July 17, 2023, 2:24pm UTC](https://community.brain-map.org/t/abc-atlas-user-guide-mouse-whole-brain-transcriptomic-cell-type-atlas-data-and-dimensions/2445/3 "2023-07-17T14:24:22Z")
Hi @Elysha-AIBS , I am trying to retrieve the data from the amazon web services bucket, I noticed that when I’m running the retrieval code in the python notebook from GitHub, my code runs for retrieval, however I notice the runtime is 0.0 seconds, and when I check my destination folder, I can’t locate the files from the AWS bucket. Is there any assistance to this end? Thanks, MP ---
**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:** [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/2445/4 "2023-07-18T15:00:47Z")
Hi @MPanday, Can you paste a screenshot of your notebook here of these 2 cells? ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/70c96e454b91f105ac690202995c7a1f3c768750.png)