# How To **URL:** https://community.brain-map.org/c/how-to/15.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 --- ## [\[May 2026\] Latest BICAN consortium data now available in BKP Data Catalog](https://community.brain-map.org/t/may-2026-latest-bican-consortium-data-now-available-in-bkp-data-catalog/4841)
**Author:** [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Replies:** 0\ **Last updated:** [February 3, 2026, 6:47pm UTC](https://community.brain-map.org/t/may-2026-latest-bican-consortium-data-now-available-in-bkp-data-catalog/4841 "2026-02-03T18:47:12Z")
The Allen Institute for Brain Science is excited to share its latest release with the neuroscience community: the second public release of single cell transcriptomic and epigenomic post-QC data from the BRAIN Initiative … --- ## [New Feature in ABC Atlas: Filter multiple genes at once](https://community.brain-map.org/t/new-feature-in-abc-atlas-filter-multiple-genes-at-once/4832)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [January 20, 2026, 10:24pm UTC](https://community.brain-map.org/t/new-feature-in-abc-atlas-filter-multiple-genes-at-once/4832 "2026-01-20T22:24:23Z")
The ABC Atlas has been updated to allow users to apply more than one gene filter to the same view. Filtering by multiple genes Previously ABC Atlas was limited to one gene expression filter at a time. Now, you can filt… --- ## [Downloading 3-D Expression Grid Data](https://community.brain-map.org/t/downloading-3-d-expression-grid-data/2859)
**Author:** [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Replies:** 1\ **Last updated:** [January 12, 2026, 1:52am UTC](https://community.brain-map.org/t/downloading-3-d-expression-grid-data/2859 "2026-01-12T01:52:06Z")
Download 3-D expression grid data packaged into a compressed archive file (.zip). Prototype http://api.brain-map.org/grid\_data/download/\[SectionDataSet.id\]&include=\[images\] Examples Download the 200um density volume f… --- ## [How to: BrainSpan Atlas of the Developing Human Brain](https://community.brain-map.org/t/how-to-brainspan-atlas-of-the-developing-human-brain/2890)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 1\ **Last updated:** [December 29, 2025, 1:33pm UTC](https://community.brain-map.org/t/how-to-brainspan-atlas-of-the-developing-human-brain/2890 "2025-12-29T13:33:32Z")
This is the online help for the BrainSpan Atlas of the Developing Human Brain web application. The BrainSpan Atlas of the Developing Human Brain is designed as a foundational resource for studying transcriptional mechan… --- ## [RNA-sequencing of the Aging, Dementia and TBI Project](https://community.brain-map.org/t/rna-sequencing-of-the-aging-dementia-and-tbi-project/3044)
**Author:** [@Susan.Sunkin](https://community.brain-map.org/u/Susan.Sunkin)\ **Replies:** 1\ **Last updated:** [December 19, 2025, 8:04pm UTC](https://community.brain-map.org/t/rna-sequencing-of-the-aging-dementia-and-tbi-project/3044 "2025-12-19T20:04:04Z")
RNA-Sequencing Searching Gene Search Differential Search Donor Selection Search Results Metadata Summary Heatmap Viewer Correlative Search Genome Browser To complement the protein quantification and histologic… --- ## [Documentation: BrainSpan Atlas of the Developing Human Brain](https://community.brain-map.org/t/documentation-brainspan-atlas-of-the-developing-human-brain/2897)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 5\ **Last updated:** [December 9, 2025, 4:17pm UTC](https://community.brain-map.org/t/documentation-brainspan-atlas-of-the-developing-human-brain/2897 "2025-12-09T16:17:56Z")
Documentation for BrainSpan Document Description Developmental Transcriptome Overview of methods for transcriptome profiling Prenatal LMD Microarray Overview of methods for prenatal laser microdissection microa… --- ## [Cell Types Database: Physiology and Morphology](https://community.brain-map.org/t/cell-types-database-physiology-and-morphology/2987)
**Author:** [@rachel.hostetler](https://community.brain-map.org/u/rachel.hostetler)\ **Replies:** 15\ **Last updated:** [December 8, 2025, 9:28pm UTC](https://community.brain-map.org/t/cell-types-database-physiology-and-morphology/2987 "2025-12-08T21:28:14Z")
Physiology and morphology Searching the database Filters Parallel coordinate plot of cell features Cell summary cards Electrophysiology details page Morphology details page Neuronal models Data access and download S… --- ## [ABC Anatomic Location Mapping Question](https://community.brain-map.org/t/abc-anatomic-location-mapping-question/4747)
**Author:** [@qpandas](https://community.brain-map.org/u/qpandas)\ **Replies:** 3\ **Last updated:** [December 1, 2025, 9:38pm UTC](https://community.brain-map.org/t/abc-anatomic-location-mapping-question/4747 "2025-12-01T21:38:24Z")
Hello, I am trying to understand the nomenclature that ABC uses for their regions of interests - specifically, I see that some use the Allen Brain Atlas nomenclature while some areas utilize the Modified Brodmann. I’m s… --- ## [Question: Performance of Shunt for Hydrocephalus at High Altitudes](https://community.brain-map.org/t/question-performance-of-shunt-for-hydrocephalus-at-high-altitudes/1912)
**Author:** [@LindsayCaron](https://community.brain-map.org/u/LindsayCaron)\ **Replies:** 6\ **Last updated:** [November 29, 2025, 9:15pm UTC](https://community.brain-map.org/t/question-performance-of-shunt-for-hydrocephalus-at-high-altitudes/1912 "2025-11-29T21:15:47Z")
Hello! I am a recent survivor of a Severe TBI. I acquired Hydrocephalus and now have a VP Shunt, set at the lowest (thus hardest pumping) setting. Is high altitude safe with a Shunt alleviating Hydrocephalus or for brain… --- ## [Brain Span bulk RNA-Seq data](https://community.brain-map.org/t/brain-span-bulk-rna-seq-data/4767)
**Author:** [@xyaous](https://community.brain-map.org/u/xyaous)\ **Replies:** 1\ **Last updated:** [November 14, 2025, 10:47pm UTC](https://community.brain-map.org/t/brain-span-bulk-rna-seq-data/4767 "2025-11-14T22:47:51Z")
Is there a plan, or would you consider, reprocessing the RNA-Seq data or making its fastq data available to the community? The current gencode-based release is more than 10 years old, and many exon/gene definitions hav… --- ## [Accessing the new CellTransformer dataset?](https://community.brain-map.org/t/accessing-the-new-celltransformer-dataset/4756)
**Author:** [@agidwani64](https://community.brain-map.org/u/agidwani64)\ **Replies:** 1\ **Last updated:** [November 12, 2025, 8:28pm UTC](https://community.brain-map.org/t/accessing-the-new-celltransformer-dataset/4756 "2025-11-12T20:28:37Z")
I just read the CellTransformer collaboration paper (UCSF-Allen), and thought it might be interesting to examine how the AI model’s region definitions align with discoveries I have made using the ABC Atlas dataset. Is th… --- ## [New Features in the ABC Atlas](https://community.brain-map.org/t/new-features-in-the-abc-atlas/4759)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [November 12, 2025, 12:36am UTC](https://community.brain-map.org/t/new-features-in-the-abc-atlas/4759 "2025-11-12T00:36:37Z")
The ABC Atlas has been updated with new features. View Marker Gene Expression from Cell Type Cards When viewing Marker Genes on Cell Types gene sets can now be added to the gene panel for visualizing gene expression in… --- ## [ABC Atlas Assistant Technical Documentation](https://community.brain-map.org/t/abc-atlas-assistant-technical-documentation/4758)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [November 12, 2025, 12:31am UTC](https://community.brain-map.org/t/abc-atlas-assistant-technical-documentation/4758 "2025-11-12T00:31:48Z")
Overview Release version 1.0.0 The ABC Atlas Assistant is an AI-driven assistant that enables users to interact with ABC Atlas datasets and metadata using natural language. This release establishes the foundation for c… --- ## [New HMBA Cross-Species Basal Ganglia Data Now Available in BKP](https://community.brain-map.org/t/new-hmba-cross-species-basal-ganglia-data-now-available-in-bkp/4755)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [November 11, 2025, 6:59pm UTC](https://community.brain-map.org/t/new-hmba-cross-species-basal-ganglia-data-now-available-in-bkp/4755 "2025-11-11T18:59:02Z")
The Human and Mammalian Brain Atlas (HMBA) is a major atlas of the BRAIN Initiative Cell Atlas Network (BICAN) that proposes to establish a comprehensive, highly granular cell atlas in complete adult human, macaque, and … --- ## [Introducing the ABC Atlas AI Assistant!](https://community.brain-map.org/t/introducing-the-abc-atlas-ai-assistant/4753)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [November 11, 2025, 4:16pm UTC](https://community.brain-map.org/t/introducing-the-abc-atlas-ai-assistant/4753 "2025-11-11T16:16:03Z")
The ABC Atlas Assistant is a new way to explore and visualize data in the ABC Atlas using natural language. Simply describe what you want to see and the Assistant will find the right data, apply filters or colors, and up… --- ## [Allen brain connectivity atlast not accessible](https://community.brain-map.org/t/allen-brain-connectivity-atlast-not-accessible/4751)
**Author:** [@martinvinck](https://community.brain-map.org/u/martinvinck)\ **Replies:** 1\ **Last updated:** [November 10, 2025, 8:43pm UTC](https://community.brain-map.org/t/allen-brain-connectivity-atlast-not-accessible/4751 "2025-11-10T20:43:37Z")
hi! It seems the allen brain connectivity atlas is currently offline or not accessible? We are using it for a University course, but on various browsers it seems not to be working since last week Best wishes, Martin --- ## [Access model ids from specimen\_id](https://community.brain-map.org/t/access-model-ids-from-specimen-id/4742)
**Author:** [@aquaresima](https://community.brain-map.org/u/aquaresima)\ **Replies:** 0\ **Last updated:** [November 5, 2025, 4:18pm UTC](https://community.brain-map.org/t/access-model-ids-from-specimen-id/4742 "2025-11-05T16:18:17Z")
Hello, I am trying to programmatically download a set of GLIF models that correspond to cells with specific properties (in particular, SST-positive, layer2/3). I can easily retrieve the specimen ids and run my search o… --- ## [MapMyCells Species Misidentification Issue with Unfiltered scRNA-seq Data ( rat to Bacillus megaterium)](https://community.brain-map.org/t/mapmycells-species-misidentification-issue-with-unfiltered-scrna-seq-data-rat-to-bacillus-megaterium/4731)
**Author:** [@muchangqing777](https://community.brain-map.org/u/muchangqing777)\ **Replies:** 4\ **Last updated:** [November 4, 2025, 11:26am UTC](https://community.brain-map.org/t/mapmycells-species-misidentification-issue-with-unfiltered-scrna-seq-data-rat-to-bacillus-megaterium/4731 "2025-11-04T11:26:47Z")
Problem Description I’m experiencing a puzzling issue with MapMyCells where the same rat brain snRNA-seq dataset produces completely different results depending on quality control (QC) status: Successful Case (With QC) … --- ## [Announcing the new brain-map: same high quality data in a more accessible and modern format](https://community.brain-map.org/t/announcing-the-new-brain-map-same-high-quality-data-in-a-more-accessible-and-modern-format/4725)
**Author:** [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Replies:** 0\ **Last updated:** [October 20, 2025, 7:34pm UTC](https://community.brain-map.org/t/announcing-the-new-brain-map-same-high-quality-data-in-a-more-accessible-and-modern-format/4725 "2025-10-20T19:34:33Z")
We’re very excited to announce the release of the new brain-map.org ecosystem - it replaces the pages previously available under portal.brain-map.org. Scientists continue to have access to the same high quality data and … --- ## [Genetic Tools Atlas: new thalamus and basal ganglia enhancers, macaque experiments, and SmartSPIM images](https://community.brain-map.org/t/genetic-tools-atlas-new-thalamus-and-basal-ganglia-enhancers-macaque-experiments-and-smartspim-images/4724)
**Author:** [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Replies:** 0\ **Last updated:** [October 20, 2025, 4:01pm UTC](https://community.brain-map.org/t/genetic-tools-atlas-new-thalamus-and-basal-ganglia-enhancers-macaque-experiments-and-smartspim-images/4724 "2025-10-20T16:01:49Z")
The Allen Institute for Brain Science is excited to share its latest release to the Genetic Tools Atlas (GTA). It adds a more than 750 datasets. These include 80+ mouse whole-brain light sheet microscopy images as well a… --- ## [Downloading and Displaying SVG](https://community.brain-map.org/t/downloading-and-displaying-svg/2868)
**Author:** [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Replies:** 1\ **Last updated:** [October 1, 2025, 6:07pm UTC](https://community.brain-map.org/t/downloading-and-displaying-svg/2868 "2025-10-01T18:07:36Z")
Prototype Examples Parameters Returns The SVG download service returns annotations associated with the specified SectionImage as scalable vector graphics (SVG). Examples of annotations that can be retrieved include hot… --- ## [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 --- ## [MapMyCells compressed csv failure](https://community.brain-map.org/t/mapmycells-compressed-csv-failure/4500)
**Author:** [@Maycie\_S](https://community.brain-map.org/u/Maycie_S)\ **Replies:** 9\ **Last updated:** [September 17, 2025, 8:20pm UTC](https://community.brain-map.org/t/mapmycells-compressed-csv-failure/4500 "2025-09-17T20:20:03Z")
Hello, I have successfully used the MapMyCells platform multiple times in the past and noticed recently mapping fails when I upload a compressed csv. I have not changed my code so I am wondering why this may be. To test… --- ## [New features in MapMyCells: Basal Ganglia taxonomy and cross-species mapping](https://community.brain-map.org/t/new-features-in-mapmycells-basal-ganglia-taxonomy-and-cross-species-mapping/4698)
**Author:** [@danielsf](https://community.brain-map.org/u/danielsf)\ **Replies:** 0\ **Last updated:** [September 17, 2025, 5:09pm UTC](https://community.brain-map.org/t/new-features-in-mapmycells-basal-ganglia-taxonomy-and-cross-species-mapping/4698 "2025-09-17T17:09:50Z")
We are pleased to announce two new features in MapMyCells. MapMyCells now allows users to map data onto the Consensus Basal Ganglia taxonomy, a multi-species (human, macaque, marmoset) taxonomy of cell types in the ba… --- ## [Layer-based annotation of WHB10xv3 dataset](https://community.brain-map.org/t/layer-based-annotation-of-whb10xv3-dataset/4579)
**Author:** [@marsdenl](https://community.brain-map.org/u/marsdenl)\ **Replies:** 6\ **Last updated:** [September 12, 2025, 4:45pm UTC](https://community.brain-map.org/t/layer-based-annotation-of-whb10xv3-dataset/4579 "2025-09-12T16:45:43Z")
Hey there :slight\_smile: Thank you for the WHB atlas and the associated resources, they’ve been really useful! I have isolated excitatory cortical neurons of interest from the atlas by supercluster (\[‘Deep-layer near-p… --- ## [BrainSpan API - Developmental Transcriptome](https://community.brain-map.org/t/brainspan-api-developmental-transcriptome/2895)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 3\ **Last updated:** [September 12, 2025, 2:14am UTC](https://community.brain-map.org/t/brainspan-api-developmental-transcriptome/2895 "2025-09-12T02:14:42Z")
The BrainSpan Atlas of the Developing Human Brain is a foundational resource for studying transcriptional mechanisms involved in human brain development. The data includes: Developmental Transcriptome: RNA sequencin… --- ## [How to get genes expressed in specific ROI of human brain](https://community.brain-map.org/t/how-to-get-genes-expressed-in-specific-roi-of-human-brain/4334)
**Author:** [@ajdefreese](https://community.brain-map.org/u/ajdefreese)\ **Replies:** 5\ **Last updated:** [August 26, 2025, 9:39pm UTC](https://community.brain-map.org/t/how-to-get-genes-expressed-in-specific-roi-of-human-brain/4334 "2025-08-26T21:39:01Z")
Hi! I’m trying to identify all genes expressed in the auditory cortex using the human brain atlas. What is the simplest way to do this using the online GUI? --- ## [MapMyCells fails to map, and fails to output logs](https://community.brain-map.org/t/mapmycells-fails-to-map-and-fails-to-output-logs/4672)
**Author:** [@Sverreg](https://community.brain-map.org/u/Sverreg)\ **Replies:** 2\ **Last updated:** [August 22, 2025, 1:21pm UTC](https://community.brain-map.org/t/mapmycells-fails-to-map-and-fails-to-output-logs/4672 "2025-08-22T13:21:21Z")
Hi, I ran MapMyCells in the browser yesterday, it worked perfectly. Tried a new file today and it failed, tried the same file as yesterday, it fails too. When I click download logs, I just get an xml popup in a new tab: … --- ## [\[New User\] 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… --- ## [Not able to download or view Human ISH data](https://community.brain-map.org/t/not-able-to-download-or-view-human-ish-data/4492)
**Author:** [@MPanday](https://community.brain-map.org/u/MPanday)\ **Replies:** 10\ **Last updated:** [August 19, 2025, 3:09pm UTC](https://community.brain-map.org/t/not-able-to-download-or-view-human-ish-data/4492 "2025-08-19T15:09:16Z")
Hello, I’ve been trying to access the Allen Human Brain Atlas ISH Database, and I have notived that I’m not able to view or download any image data from the website. I’m interacting with the cortex study, and this has b… [Previous page](https://community.brain-map.org/c/how-to/15.md) [Next page](https://community.brain-map.org/c/how-to/15.md?page=2)