# New Whole Human Brain Data Explorable in the ABC Atlas
**URL:** https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185
**Category:** Allen Brain Cell (ABC) Atlas
**Created:** [March 25, 2024, 4:45pm UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185 "2024-03-25T16:45:22Z")
**Posts on this page:** 11
**Page:** 1
### Author:  [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)
#### Post date: [March 25, 2024, 4:45pm UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185/1 "2024-03-25T16:45:22Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new data!
Data from [Transcriptomic diversity of cell types across the adult human brain](https://www.science.org/doi/10.1126/science.add7046)is now explorable in the ABC Atlas. This dataset includes more than three million cells sampled from the adult human brain. Samples were isolated from ~100 dissections from three donors and assayed using single-nucleus RNA sequencing. The resulting cells were clustered into hierarchical groups of 31 superclusters, 461 clusters, and 3313 subclusters. Additionally, categorical neurotransmitter type annotations were assigned to clusters based on expression (or lack thereof) of one or more neurotransmitter-associated marker genes. Included in this dataset includes two tSNE plots - one plot contains approximately 900k non-neuronal cells and the other contains approximately 2.5m neuronal cells.
- [Neurons](https://knowledge.brain-map.org/abcatlas?state=AQEBOU02NEo3UzBBM1pOSUpBNFZTNgACR1o5NFo4M1JYVVRFQ0hZS1FPNAADAAQBAQKAHGKkf3qH0QOFOtWYhURkegAFAQFUUklQMTEAAAYBAQJYM0s3SzJFRzZVTVhPTjBUOUJFAAN%2BAAAABAAACFVNWko3WkxGOEc1Rkg1UzlZNFUACUMzUlJWQUsxOEhHNlExSk42WlEACgAAAgEA)
- [Non-neuronal cells](https://knowledge.brain-map.org/abcatlas?state=AQEBOU02NEo3UzBBM1pOSUpBNFZTNgACUjVGV1VWVEVBMk9XOU5KUU1ZOQADAAQBAQKB8kv8fw2bywOFGAqchQRcfQAFAQFUUklQMTEAAAYBAQJYM0s3SzJFRzZVTVhPTjBUOUJFAAN%2BAAAABAAACDVUNEMzTUMzTE5aV0VCREZVRVoACUMzUlJWQUsxOEhHNlExSk42WlEACgAAAgEA)
Check out our [GitHub resources](https://alleninstitute.github.io/abc_atlas_access/descriptions/WHB_notebooks.html) to learn more and download data.
As always, thank you for being part of the AIBS community. Please [let us know](https://docs.google.com/forms/d/e/1FAIpQLSeIaEalEJM-sz4PYMMXNtWvLXdGceqTdfP_Qvp3DIv7uEHSFg/viewform)how we can improve the ABC Atlas to better serve your needs.
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### Author:  [@xyaous](https://community.brain-map.org/u/xyaous)
#### Post date: [June 13, 2025, 5:21am UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185/2 "2025-06-13T05:21:29Z")
Hello,
I was able to download the 20241115 version of WHB-10Xv3 dataset’s cell\_metadata file at [AWS S3 Explorer](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WHB-10Xv3/20241115/)
It looks that the metadata file listed all 3 million plus cells, but did have a column for cell type annotation. I guess that the “cluster\_alias” column can be mapped to cell type annotation.
Is there another version of the cell\_metadata file having cell type annotation, or another file having cluster\_alias to cell type annotation mapping?
Thanks in advance.
Sean
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### Author:  [@morriscb](https://community.brain-map.org/u/morriscb)
#### Post date: [June 13, 2025, 3:41pm UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185/3 "2025-06-13T15:41:54Z")
Hi Sean,
You can take a look at this tutorial jupyter notebook: [10x RNA-seq gene expression data (part 1) — Allen Brain Cell Atlas - Data Access](https://alleninstitute.github.io/abc_atlas_access/notebooks/10x_snRNASeq_tutorial_part_1.html) This is walking through joining the cell metadata tables that you’ve found with the cell type annotations and walking through some basic extraction of gene expression data. You are correct that cluster\_alias is the column that joins the cells and taxonomy/celltype annotations.
You can find a full suite of notebooks for the Whole Mouse Brain dataset here: [Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng) — Allen Brain Cell Atlas - Data Access](https://alleninstitute.github.io/abc_atlas_access/descriptions/notebook_subtitle1.html)
If you are comfortable with python, there is the classes in [this repository](https://github.com/AllenInstitute/abc_atlas_access/) that allow for more programmatic access to the data on S3 vs browsing the s3 bucket on the web. The repository also contains all of the tutorial notebooks we have which you can download and modify to your needs.
Chris
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### Author:  [@xyaous](https://community.brain-map.org/u/xyaous)
#### Post date: [June 13, 2025, 4:25pm UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185/4 "2025-06-13T16:25:54Z")
Hi Chris,
Thanks for your quick response!
I’m trying to access the WHB-10Xv3 20241115 dataset. Is it structured the same as the WMB dataset, so the notebook tutorial will work if I simply change the dataset reference?
If you have a cluster-alias to cell type mapping file handy, can you simply share it?
Best regards
Sean
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### Author:  [@morriscb](https://community.brain-map.org/u/morriscb)
#### Post date: [June 13, 2025, 5:03pm UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185/5 "2025-06-13T17:03:28Z")
Hey Sean,
Sorry about. I have the mouse data on the brain so read it as WMB-10Xv3. Here’s the equivalent set of notebooks for WHB: [Whole Human Brain 10x scRNA-seq gene expression data — Allen Brain Cell Atlas - Data Access](https://alleninstitute.github.io/abc_atlas_access/descriptions/WHB_notebooks.html)
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### Author:  [@xyaous](https://community.brain-map.org/u/xyaous)
#### Post date: [June 13, 2025, 6:04pm UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185/6 "2025-06-13T18:04:42Z")
Hi Chris,
The tutorial was very clear. I was able to load the correct manifest and retrieve both the metadata term and membership datasets from WHB-taxonomy.
Thank you so much for your prompt support and for the invaluable work done by the Allen Institute.
Best regards,
Sean
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### Author:  [@xyaous](https://community.brain-map.org/u/xyaous)
#### Post date: [June 16, 2025, 5:58am UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185/7 "2025-06-16T05:58:35Z")
Hi,
Thank you for your detailed tutorial and support. I was able to retrieve my genes of interest from the WHB-10Xv3 20241115 dataset.
Since the dataset contains over 3 million cells, I’m looking to filter for subsets based on QC metrics and homogeneity in each cell types. Is there mapping data available for each cell, such as the number of reads mapped and the number of genes detected?
Best regards,
Sean
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### Author:  [@morriscb](https://community.brain-map.org/u/morriscb)
#### Post date: [June 16, 2025, 4:56pm UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185/8 "2025-06-16T16:56:33Z")
Hi Sean, could you post this question as a new thread? Your question and the answer may be helpful for other folks right now it may be lost under this original announcement post where people may not expect to look. Thanks!
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### Author:  [@xyaous](https://community.brain-map.org/u/xyaous)
#### Post date: [June 16, 2025, 5:40pm UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185/9 "2025-06-16T17:40:37Z")
Just did a new topic. Thx!
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### Author:  [@DNijhof](https://community.brain-map.org/u/DNijhof)
#### Post date: [February 4, 2026, 3:46pm UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185/10 "2026-02-04T15:46:37Z")
Hello,
I am exploring this dataset and was wondering about the log2 normalised data, I couldn’t find a specific description in the Siletti paper on how this was done. Is it a basic log2 normalisation and has any scaling been done?
Thank you in advance.
Best wishes,
D
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### Author:  [@danielsf](https://community.brain-map.org/u/danielsf)
#### Post date: [February 4, 2026, 4:14pm UTC](https://community.brain-map.org/t/new-whole-human-brain-data-explorable-in-the-abc-atlas/3185/11 "2026-02-04T16:14:46Z")
The “log2” dataset is “log2(counts per million + 1)”
So, for each cell:
1. take the expression vector in the “raw” dataset
2. multiply by whatever factor is needed to get the sum of the vector to equal 1 million
3. add one (so that you never have to take the log of zero)
4. take log2 of the vector from (3)