# \#human **URL:** https://community.brain-map.org/tag/human/71.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) --- ## [Clarification of SEA-AD MTG layer-level IBA1–6E10 colocalization percentage](https://community.brain-map.org/t/clarification-of-sea-ad-mtg-layer-level-iba1-6e10-colocalization-percentage/5068)
**Author:** [@Alexy](https://community.brain-map.org/u/Alexy)\ **Replies:** 0\ **Last updated:** [September 5, 2026, 9:23pm UTC](https://community.brain-map.org/t/clarification-of-sea-ad-mtg-layer-level-iba1-6e10-colocalization-percentage/5068 "2026-09-05T21:23:09Z")
Hello SEA-AD team, I am preparing a donor-level secondary analysis using the publicly released June 2026 SEA-AD quantitative neuropathology summary and processed MTG endothelial pseudobulk data. I would appreciate clari… --- ## [Unable to download the normalized microarray dataset for donor H0351.1015](https://community.brain-map.org/t/unable-to-download-the-normalized-microarray-dataset-for-donor-h0351-1015/5004)
**Author:** [@Maria.YH.Lee](https://community.brain-map.org/u/Maria.YH.Lee)\ **Replies:** 1\ **Last updated:** [August 10, 2026, 4:50pm UTC](https://community.brain-map.org/t/unable-to-download-the-normalized-microarray-dataset-for-donor-h0351-1015/5004 "2026-08-10T16:50:36Z")
When I try to download the microarray dataset containing gene expression values for donor H0351.1015, I receive the following message: “The page you were looking for doesn’t exist. You may have mistyped the address or th… --- ## [Human Brain Atlas Mesh Files](https://community.brain-map.org/t/human-brain-atlas-mesh-files/560)
**Author:** [@jopeter](https://community.brain-map.org/u/jopeter)\ **Replies:** 6\ **Last updated:** [June 2, 2026, 4:42am UTC](https://community.brain-map.org/t/human-brain-atlas-mesh-files/560 "2026-06-02T04:42:52Z")
Hello, I was wondering if the Allen Institute provides structural meshes for a segmented human reference brain similar to the mouse ccf meshes provided here: http://download.alleninstitute.org/informatics-archive/curren… --- ## [Issue matching cells with their metadata from SEA-AD spatial transcriptomics datasets](https://community.brain-map.org/t/issue-matching-cells-with-their-metadata-from-sea-ad-spatial-transcriptomics-datasets/2977)
**Author:** [@tson](https://community.brain-map.org/u/tson)\ **Replies:** 5\ **Last updated:** [February 18, 2026, 9:07pm UTC](https://community.brain-map.org/t/issue-matching-cells-with-their-metadata-from-sea-ad-spatial-transcriptomics-datasets/2977 "2026-02-18T21:07:05Z")
I hope this message finds you well. I am reaching out to bring to your attention a potential discrepancy we have observed related to the SEA-AD MERFISH spatial transcriptomics datasets. Specifically, it is not clear to u… --- ## [Allen Human Reference Atlas - 3D, 2020 (new!)](https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405)
**Author:** [@Carol](https://community.brain-map.org/u/Carol)\ **Replies:** 20\ **Last updated:** [December 12, 2025, 10:49am UTC](https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405 "2025-12-12T10:49:40Z")
ALLEN HUMAN REFERENCE ATLAS - 3D, 2020 Version 1.0.0 The Allen Human Reference Atlas - 3D is a parcellation of the adult human brain in 3D, labeling every voxel with a brain structure spanning 141 structures. These parce… --- ## [How do I download specific cell type gene expression data from WHB?](https://community.brain-map.org/t/how-do-i-download-specific-cell-type-gene-expression-data-from-whb/3648)
**Author:** [@atown](https://community.brain-map.org/u/atown)\ **Replies:** 2\ **Last updated:** [September 9, 2024, 6:34pm UTC](https://community.brain-map.org/t/how-do-i-download-specific-cell-type-gene-expression-data-from-whb/3648 "2024-09-09T18:34:58Z")
Thank you for the Allen Brain cell atlas data access tool! Is there a way to download a subset of the gene expression raw data? For example, looking at a specific cell type of interest such as Astrocytes. I saw that you … --- ## [Single Neuron Theory Of Consciousness](https://community.brain-map.org/t/single-neuron-theory-of-consciousness/1100)
**Author:** [@Cameron](https://community.brain-map.org/u/Cameron)\ **Replies:** 9\ **Last updated:** [July 17, 2022, 2:49am UTC](https://community.brain-map.org/t/single-neuron-theory-of-consciousness/1100 "2022-07-17T02:49:29Z")
Hello, Senior at Port Townsend High School in Washington State here. I’ve been reading up a bit on theories on consciousness, and I’ve come across a couple that worry me, hoping to get a neuroscientist’s take on this. I… --- ## [Human Reference Atlas Right Hemisphere](https://community.brain-map.org/t/human-reference-atlas-right-hemisphere/595)
**Author:** [@jopeter](https://community.brain-map.org/u/jopeter)\ **Replies:** 2\ **Last updated:** [March 8, 2024, 11:12am UTC](https://community.brain-map.org/t/human-reference-atlas-right-hemisphere/595 "2024-03-08T11:12:20Z")
Hello, Do there exist files for the right hemisphere of the human reference atlas? Thanks, Jonah --- ## [Donor information - cause of death, healthy donors?](https://community.brain-map.org/t/donor-information-cause-of-death-healthy-donors/2909)
**Author:** [@ksiemens](https://community.brain-map.org/u/ksiemens)\ **Replies:** 1\ **Last updated:** [January 16, 2024, 7:51pm UTC](https://community.brain-map.org/t/donor-information-cause-of-death-healthy-donors/2909 "2024-01-16T19:51:47Z")
I am looking for information on the donors used in the microarray dataset (H0351.2001, H0351.2002, H0351,1009, H0351.1012, H0351.1015, H0351.1016). I see the age, sex, ethnicity and PMI. Is there any further information… --- ## [Detailed patient donor details table available?](https://community.brain-map.org/t/detailed-patient-donor-details-table-available/1975)
**Author:** [@Thijs](https://community.brain-map.org/u/Thijs)\ **Replies:** 3\ **Last updated:** [May 2, 2023, 2:02pm UTC](https://community.brain-map.org/t/detailed-patient-donor-details-table-available/1975 "2023-05-02T14:02:38Z")
Hi, Is there a detailed table of patient information available? In the TECHNICAL WHITE PAPER: CASE QUALIFICATION AND DONOR PROFILES, the table is rather limited and seems to be missing details that were recorded. For i… --- ## [Downloading and exploring -omics data from SEA-AD](https://community.brain-map.org/t/downloading-and-exploring-omics-data-from-sea-ad/1964)
**Author:** [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)\ **Replies:** 2\ **Last updated:** [February 2, 2023, 5:11pm UTC](https://community.brain-map.org/t/downloading-and-exploring-omics-data-from-sea-ad/1964 "2023-02-02T17:11:36Z")
The Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) consortium strives to gain a deep molecular and cellular understanding of the early pathogenesis of Alzheimer’s disease. As part of this effort, \>2 million cells … --- ## [Varying Probes number depending on contrast structure](https://community.brain-map.org/t/varying-probes-number-depending-on-contrast-structure/2079)
**Author:** [@waltheja](https://community.brain-map.org/u/waltheja)\ **Replies:** 2\ **Last updated:** [January 16, 2023, 12:47pm UTC](https://community.brain-map.org/t/varying-probes-number-depending-on-contrast-structure/2079 "2023-01-16T12:47:34Z")
Dear users, i want to compare expression levels with the differential search tool form the human microarray platform (Microarray Data :: Allen Brain Atlas: Human Brain). The number of analyzed probes varies when i cha… --- ## [Comparing gene expression between two structures using log2(intensity) values](https://community.brain-map.org/t/comparing-gene-expression-between-two-structures-using-log2-intensity-values/1919)
**Author:** [@Carlos](https://community.brain-map.org/u/Carlos)\ **Replies:** 4\ **Last updated:** [October 21, 2022, 7:10pm UTC](https://community.brain-map.org/t/comparing-gene-expression-between-two-structures-using-log2-intensity-values/1919 "2022-10-21T19:10:06Z")
Hi all! I am new to this forum and to gene expression analysis, being this the first time I use data from the Allen Human Brain Atlas. I am trying to compare the expression of a particular gene (e.g. GRIN1) between two … --- ## [Normalized Microarray Datasets](https://community.brain-map.org/t/normalized-microarray-datasets/1881)
**Author:** [@waltheja](https://community.brain-map.org/u/waltheja)\ **Replies:** 3\ **Last updated:** [October 19, 2022, 3:21pm UTC](https://community.brain-map.org/t/normalized-microarray-datasets/1881 "2022-10-19T15:21:48Z")
Hello everybody, i want to use the following normalized microarray datasets (Microarray Data Download :: Allen Brain Atlas: Human Brain) to perform a differential gene analysis on specific anatomical region of the brain… --- ## [Bvec and bval files available for human diffusion MRI?](https://community.brain-map.org/t/bvec-and-bval-files-available-for-human-diffusion-mri/1744)
**Author:** [@aslanabivardi](https://community.brain-map.org/u/aslanabivardi)\ **Replies:** 2\ **Last updated:** [August 11, 2022, 9:17am UTC](https://community.brain-map.org/t/bvec-and-bval-files-available-for-human-diffusion-mri/1744 "2022-08-11T09:17:51Z")
Hi there, I would like to run a tractography analysis on the highresolution diffusion MRI data from the BrainSpan Reference Atlas, specifically the 34 yrs human data due to the rare combination of with the Parvalbumin s… --- ## [Brain region dissection procedures](https://community.brain-map.org/t/brain-region-dissection-procedures/1715)
**Author:** [@teddyd](https://community.brain-map.org/u/teddyd)\ **Replies:** 2\ **Last updated:** [July 28, 2022, 5:25pm UTC](https://community.brain-map.org/t/brain-region-dissection-procedures/1715 "2022-07-28T17:25:27Z")
Hello, I hope that you are staying well. I am exploring the Developmental Transcriptome and have some questions about the specifications for the striatum brain region. Within the interactive atlas, the striatum includes… --- ## [Is smart-seq matrix human multiple cortical areas normalized?](https://community.brain-map.org/t/is-smart-seq-matrix-human-multiple-cortical-areas-normalized/1703)
**Author:** [@StanDriessens](https://community.brain-map.org/u/StanDriessens)\ **Replies:** 1\ **Last updated:** [July 18, 2022, 3:36pm UTC](https://community.brain-map.org/t/is-smart-seq-matrix-human-multiple-cortical-areas-normalized/1703 "2022-07-18T15:36:25Z")
Hi, Can someone clarify if the counts in the smart-seq matrices for human cell types have been normalized (CPM)? If not is this dataset also available for normalized values? Thanks! Stan --- ## [Correlation between brain structure and sample ID in microarray.csv](https://community.brain-map.org/t/correlation-between-brain-structure-and-sample-id-in-microarray-csv/1551)
**Author:** [@waltheja](https://community.brain-map.org/u/waltheja)\ **Replies:** 1\ **Last updated:** [March 31, 2022, 4:30pm UTC](https://community.brain-map.org/t/correlation-between-brain-structure-and-sample-id-in-microarray-csv/1551 "2022-03-31T16:30:34Z")
Hello, i want to use the microarrryExpression.csv data file to examine the expression profile of specific brain regions. How can i assign the sample id (e.g. X3.6157916807089787 in the first column) to a specific brain … --- ## [RNAseq data of the Brain Span Atlas of the Human Brain - confirmation of the method](https://community.brain-map.org/t/rnaseq-data-of-the-brain-span-atlas-of-the-human-brain-confirmation-of-the-method/1404)
**Author:** [@Macuchova](https://community.brain-map.org/u/Macuchova)\ **Replies:** 1\ **Last updated:** [January 6, 2022, 3:57pm UTC](https://community.brain-map.org/t/rnaseq-data-of-the-brain-span-atlas-of-the-human-brain-confirmation-of-the-method/1404 "2022-01-06T15:57:56Z")
Dear All, I have been annotating and analyzing the RNAseq data of the Brain Span Atlas of the Human Brain, downloaded from dbGaP under Study Accession: phs000755.v2.p1. Data, as saved in the SRA repository Studies : Br… --- ## [References and citations of human RNA-seq datasets](https://community.brain-map.org/t/references-and-citations-of-human-rna-seq-datasets/1323)
**Author:** [@nmeo](https://community.brain-map.org/u/nmeo)\ **Replies:** 1\ **Last updated:** [November 5, 2021, 7:11pm UTC](https://community.brain-map.org/t/references-and-citations-of-human-rna-seq-datasets/1323 "2021-11-05T19:11:38Z")
Hello, I have 2 questions about the original source of the snRNAdata that I appreciate your help to figure them out: The technical white paper, including the details about the postmortem subjects, provieded for “M1” … --- ## [DTT in nuclei isolation](https://community.brain-map.org/t/dtt-in-nuclei-isolation/1028)
**Author:** [@Martina17](https://community.brain-map.org/u/Martina17)\ **Replies:** 1\ **Last updated:** [April 13, 2021, 9:24pm UTC](https://community.brain-map.org/t/dtt-in-nuclei-isolation/1028 "2021-04-13T21:24:54Z")
Hi, I am working with isolation of nuclei from human prefrontal cortex. The protocol I am currently using can be summarized as follows: tissue homogenization using dounce homogenizer followed by a clean-up that is carr… --- ## [Question regarding Section position within specimen in Human Brain](https://community.brain-map.org/t/question-regarding-section-position-within-specimen-in-human-brain/977)
**Author:** [@lintek](https://community.brain-map.org/u/lintek)\ **Replies:** 2\ **Last updated:** [March 16, 2021, 8:02pm UTC](https://community.brain-map.org/t/question-regarding-section-position-within-specimen-in-human-brain/977 "2021-03-16T20:02:03Z")
Hi, I would like to use the ISH data from Allen Brain for a project specifically I am looking at CALB1 in the visual cortex. When I click on a specimen I am taken to the following page for example: http://human.brain-… --- ## [Download Section Dataset Images from Brainspan ISH with gene/probe and donor age metadata](https://community.brain-map.org/t/download-section-dataset-images-from-brainspan-ish-with-gene-probe-and-donor-age-metadata/941)
**Author:** [@carmen.se](https://community.brain-map.org/u/carmen.se)\ **Replies:** 1\ **Last updated:** [March 8, 2021, 8:06pm UTC](https://community.brain-map.org/t/download-section-dataset-images-from-brainspan-ish-with-gene-probe-and-donor-age-metadata/941 "2021-03-08T20:06:21Z")
Hi, I am trying to get all the Brainspan ISH images for all Section Datasets belonging to prenatal ages (3 donors) and only from 3 strcutures: visual cortex, prefrontal cortex, and ‘brain’. i.e., the experiments liste… --- ## [\[Brainspan ISH\] Atlas Image to Section Image](https://community.brain-map.org/t/brainspan-ish-atlas-image-to-section-image/956)
**Author:** [@carmen.se](https://community.brain-map.org/u/carmen.se)\ **Replies:** 1\ **Last updated:** [February 26, 2021, 4:39pm UTC](https://community.brain-map.org/t/brainspan-ish-atlas-image-to-section-image/956 "2021-02-26T16:39:05Z")
Hi, I would like to retrieve the list of section\_images corresponding to a list of reference images for a specific atlas, but I can’t figure out how to do this. For example, for atlas\_id 138322603 , the pcw 15 developi… --- ## [Quantified ISH data for autism & schizophrenia studies](https://community.brain-map.org/t/quantified-ish-data-for-autism-schizophrenia-studies/638)
**Author:** [@ajuavinett](https://community.brain-map.org/u/ajuavinett)\ **Replies:** 2\ **Last updated:** [November 18, 2020, 6:38pm UTC](https://community.brain-map.org/t/quantified-ish-data-for-autism-schizophrenia-studies/638 "2020-11-18T18:38:24Z")
Hey technical team! My understanding is that some but not all of the ISH data has quantification by brain area, or at least some sort of grid with intensity values, right? I was trying to see if this was available for t… --- ## [How to set median data in transcriptomics explorer in human datasets?](https://community.brain-map.org/t/how-to-set-median-data-in-transcriptomics-explorer-in-human-datasets/601)
**Author:** [@Christos](https://community.brain-map.org/u/Christos)\ **Replies:** 8\ **Last updated:** [November 3, 2020, 8:57pm UTC](https://community.brain-map.org/t/how-to-set-median-data-in-transcriptomics-explorer-in-human-datasets/601 "2020-11-03T20:57:57Z")
How to set median data in transcriptomics explorer in human datasets? Currently, only trimmed mean data are visible in the heatmap. --- ## [Images of capillaries in the human choroid plexus](https://community.brain-map.org/t/images-of-capillaries-in-the-human-choroid-plexus/742)
**Author:** [@Arie](https://community.brain-map.org/u/Arie)\ **Replies:** 2\ **Last updated:** [October 27, 2020, 7:36pm UTC](https://community.brain-map.org/t/images-of-capillaries-in-the-human-choroid-plexus/742 "2020-10-27T19:36:27Z")
Hello, I searched the literature for either EM, SEM, or optical images that visualize the blood vessels down to the capillary level inside the human choroid plexus. Surprisingly, there are very few of those. I found a s… --- ## [Mapping the Human Brain](https://community.brain-map.org/t/mapping-the-human-brain/325)
**Author:** [@MaroonGomes](https://community.brain-map.org/u/MaroonGomes)\ **Replies:** 1\ **Last updated:** [October 31, 2019, 4:01pm UTC](https://community.brain-map.org/t/mapping-the-human-brain/325 "2019-10-31T16:01:23Z")
I feel this area really doesn’t get enough attention. In my opinion, being able to essentially upload someone’s brain onto a computer and combining that data with brain machine interfaces will definitely become something… --- ## [DRG (dorsal root ganglion) sc/sn RNAseq profiling from NHP and humans](https://community.brain-map.org/t/drg-dorsal-root-ganglion-sc-sn-rnaseq-profiling-from-nhp-and-humans/642)
**Author:** [@ainej](https://community.brain-map.org/u/ainej)\ **Replies:** 2\ **Last updated:** [August 12, 2020, 2:59pm UTC](https://community.brain-map.org/t/drg-dorsal-root-ganglion-sc-sn-rnaseq-profiling-from-nhp-and-humans/642 "2020-08-12T14:59:04Z")
Dear Allen Brain Institute and Community, I am looking for sc/snRNAseq of human and/or NHP DRG. Although, anatomically, this is not CNS, but PNS, due to similarity in cell types/connection with CNS, I wonder if somebody… --- ## [Allen Gene Expression Datasets](https://community.brain-map.org/t/allen-gene-expression-datasets/625)
**Author:** [@ajuavinett](https://community.brain-map.org/u/ajuavinett)\ **Replies:** 2\ **Last updated:** [July 7, 2020, 4:06pm UTC](https://community.brain-map.org/t/allen-gene-expression-datasets/625 "2020-07-07T16:06:04Z")
Hi all! I’m trying to create a summary for my students (and other possible dataset users!) of all of the gene expression data available via the Allen Institute. I’d love your input on this and feedback on whether I’m mis… [Next page](https://community.brain-map.org/tag/human/71.md?match_all_tags=true&page=1&tags%5B%5D=human)