# Latest **URL:** https://community.brain-map.org/latest.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) --- ## [Community Guidelines](https://community.brain-map.org/t/community-guidelines/5)
**Author:** [@system](https://community.brain-map.org/u/system)\ **Replies:** 0\ **Last updated:** [April 19, 2018, 10:07pm UTC](https://community.brain-map.org/t/community-guidelines/5 "2018-04-19T22:07:14Z")
This is a Civilized Place for Public Discussion Please treat this discussion forum with the same respect you would a public park. We, too, are a shared community resource — a place to share skills, knowledge and inter… --- ## [Welcome to the Allen Brain Map Community Forum!](https://community.brain-map.org/t/welcome-to-the-allen-brain-map-community-forum/8)
**Author:** [@system](https://community.brain-map.org/u/system)\ **Replies:** 0\ **Last updated:** [April 19, 2018, 10:07pm UTC](https://community.brain-map.org/t/welcome-to-the-allen-brain-map-community-forum/8 "2018-04-19T22:07:15Z")
This forum is for users of the Allen Institute’s data, tools and resources to interact with one another, and learn from the creators of these amazing open resources. Ground rules and reminders Please be sure to revie… --- ## [Which segments are viewable on the Human Brain Atlas Neuroglancer viewers? (use for teaching neuroanatomy)](https://community.brain-map.org/t/which-segments-are-viewable-on-the-human-brain-atlas-neuroglancer-viewers-use-for-teaching-neuroanatomy/5030)
**Author:** [@monicathieu](https://community.brain-map.org/u/monicathieu)\ **Replies:** 7\ **Last updated:** [September 22, 2026, 6:51pm UTC](https://community.brain-map.org/t/which-segments-are-viewable-on-the-human-brain-atlas-neuroglancer-viewers-use-for-teaching-neuroanatomy/5030 "2026-09-22T18:51:49Z")
Hi there, I am teaching an undergraduate course with a neuroanatomy module for which I’d like to have students learn regions of interest by navigating a 3D brain viewer with anatomical annotations highlighted on the bra… --- ## [Missing CCF coordinates for 198,847 cells in MERFISH-C57BL6J-638850 – availability of registration transforms?](https://community.brain-map.org/t/missing-ccf-coordinates-for-198-847-cells-in-merfish-c57bl6j-638850-availability-of-registration-transforms/5081)
**Author:** [@oliver.schmitt](https://community.brain-map.org/u/oliver.schmitt)\ **Replies:** 3\ **Last updated:** [September 22, 2026, 7:50am UTC](https://community.brain-map.org/t/missing-ccf-coordinates-for-198-847-cells-in-merfish-c57bl6j-638850-availability-of-registration-transforms/5081 "2026-09-22T07:50:53Z")
Dear Allen Brain Cell Atlas / CCF registration team, I am currently integrating the whole-brain MERFISH dataset MERFISH-C57BL6J-638850 with the Allen Mouse CCF and an existing mouse brain connectome/ontology database. D… --- ## [Which MNI152 template was used for the AHBA mni\_x/y/z coordinates?](https://community.brain-map.org/t/which-mni152-template-was-used-for-the-ahba-mni-x-y-z-coordinates/5079)
**Author:** [@xingyufeng64](https://community.brain-map.org/u/xingyufeng64)\ **Replies:** 0\ **Last updated:** [September 20, 2026, 10:17pm UTC](https://community.brain-map.org/t/which-mni152-template-was-used-for-the-ahba-mni-x-y-z-coordinates/5079 "2026-09-20T22:17:40Z")
Hi everyone, I’m working with the Allen Human Brain Atlas (AHBA) microarray dataset and would like to clarify the exact standard space used for the sample coordinates in SampleAnnot.csv. Specifically, I’m referring to … --- ## [How to start/do WGCNA of microarray datasets?](https://community.brain-map.org/t/how-to-start-do-wgcna-of-microarray-datasets/5073)
**Author:** [@Navy](https://community.brain-map.org/u/Navy)\ **Replies:** 1\ **Last updated:** [September 18, 2026, 9:01am UTC](https://community.brain-map.org/t/how-to-start-do-wgcna-of-microarray-datasets/5073 "2026-09-18T09:01:13Z")
i have four datasets whcih i worked on, i used limma as they were mcroarray platforms. then i did GSE for each dataset, also did several other downstream in silico test etc. but my guide said she want me to perform wgcna… --- ## [Create 3D images?](https://community.brain-map.org/t/create-3d-images/3419)
**Author:** [@sabrawer](https://community.brain-map.org/u/sabrawer)\ **Replies:** 5\ **Last updated:** [September 14, 2026, 1:49pm UTC](https://community.brain-map.org/t/create-3d-images/3419 "2026-09-14T13:49:40Z")
Is there software to convert the coronal sections of the human brain atlas to 3D versions? I am interested in smaller areas of a few (5 - 10) successive sections. If not, is there a recommended CAD program to do this? --- ## [Permission to Archive vdFISH on Zenodo Using Allen Brain Cell Atlas–Derived Data](https://community.brain-map.org/t/permission-to-archive-vdfish-on-zenodo-using-allen-brain-cell-atlas-derived-data/5057)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 4\ **Last updated:** [September 9, 2026, 9:52pm UTC](https://community.brain-map.org/t/permission-to-archive-vdfish-on-zenodo-using-allen-brain-cell-atlas-derived-data/5057 "2026-09-09T21:52:48Z")
Dear Allen Institute Team, I have developed a non-commercial academic web application called vdFISH (virtual double fluorescence in situ hybridization), which allows users to visualize the spatial expression and co-expr… --- ## [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… --- ## [New! SEA-AD Multiregion and Caudate data now explorable in ABC Atlas](https://community.brain-map.org/t/new-sea-ad-multiregion-and-caudate-data-now-explorable-in-abc-atlas/5065)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [September 4, 2026, 7:05pm UTC](https://community.brain-map.org/t/new-sea-ad-multiregion-and-caudate-data-now-explorable-in-abc-atlas/5065 "2026-09-04T19:05:28Z")
The ABC Atlas has been updated with new data! Two new data sets from the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) are now explorable: SEA-AD Multiregion and SEA-AD CaH. SEA-AD Multiregion Taxonomy Alzheim… --- ## [Testing Research](https://community.brain-map.org/t/testing-research/4843)
**Author:** [@NowyouseeJamie](https://community.brain-map.org/u/NowyouseeJamie)\ **Replies:** 1\ **Last updated:** [September 3, 2026, 12:09pm UTC](https://community.brain-map.org/t/testing-research/4843 "2026-09-03T12:09:32Z")
I am seeking to engage with members of the Allen Brain Map and broader neuroscience research community to explore a structured, I am offering my participation as a long-term, well-documented case study to support method … --- ## [Issue with MapMyCells website?](https://community.brain-map.org/t/issue-with-mapmycells-website/5053)
**Author:** [@jungeji99](https://community.brain-map.org/u/jungeji99)\ **Replies:** 4\ **Last updated:** [September 1, 2026, 8:26pm UTC](https://community.brain-map.org/t/issue-with-mapmycells-website/5053 "2026-09-01T20:26:59Z")
Hello. I am currently bumping into an issue where a message of 'Mapping Failed’is popping up. I was wondering if it might be caused by an internal change in the website, as this issue is occurring for datasets that I hav… --- ## [Mapping Failed — application error, plus unable to download logs (Access Denied)](https://community.brain-map.org/t/mapping-failed-application-error-plus-unable-to-download-logs-access-denied/5060)
**Author:** [@lberasain](https://community.brain-map.org/u/lberasain)\ **Replies:** 1\ **Last updated:** [September 1, 2026, 8:06pm UTC](https://community.brain-map.org/t/mapping-failed-application-error-plus-unable-to-download-logs-access-denied/5060 "2026-09-01T20:06:10Z")
Hi! I’m getting “Mapping Failed” with “application errors” on a mouse scRNA-seq dataset, and I’m also unable to download the logs (getting an S3 “AccessDenied” error when clicking “Download logs”). Operating system and … --- ## [Question About Using and Distributing Allen Brain Cell Atlas Data in Non-Commercial Research Visualization Tools](https://community.brain-map.org/t/question-about-using-and-distributing-allen-brain-cell-atlas-data-in-non-commercial-research-visualization-tools/5054)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 1\ **Last updated:** [August 31, 2026, 6:26pm UTC](https://community.brain-map.org/t/question-about-using-and-distributing-allen-brain-cell-atlas-data-in-non-commercial-research-visualization-tools/5054 "2026-08-31T18:26:24Z")
Hello, I am developing several non-commercial research visualization tools using data from the Allen Brain Cell Atlas, including MERFISH and imputed gene-expression data. These tools allow users to interactively visual… --- ## [New Sharing and Download Options in ABC Atlas](https://community.brain-map.org/t/new-sharing-and-download-options-in-abc-atlas/5051)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [August 25, 2026, 6:04pm UTC](https://community.brain-map.org/t/new-sharing-and-download-options-in-abc-atlas/5051 "2026-08-25T18:04:49Z")
The ABC Atlas has been updated to allow users to share and export each frame in a view separately. Share and export by frame Previously, the share icon copied a single link for your entire view straight to your clipboar… --- ## [Programatically upload/map my local files to cloud-based MapMyCells portal](https://community.brain-map.org/t/programatically-upload-map-my-local-files-to-cloud-based-mapmycells-portal/5050)
**Author:** [@crhodes](https://community.brain-map.org/u/crhodes)\ **Replies:** 2\ **Last updated:** [August 25, 2026, 5:09pm UTC](https://community.brain-map.org/t/programatically-upload-map-my-local-files-to-cloud-based-mapmycells-portal/5050 "2026-08-25T17:09:28Z")
Hi, Can I use the cell type mapper cli to programatically upload my local files (ex anndata/csv format) to run on the cloud-based MapMyCells tool? I would prefer to use the existing MapMyCells backend and taxonomies fo… --- ## [Deep Generative Mapping on your own machine](https://community.brain-map.org/t/deep-generative-mapping-on-your-own-machine/5049)
**Author:** [@crhodes](https://community.brain-map.org/u/crhodes)\ **Replies:** 1\ **Last updated:** [August 25, 2026, 4:51pm UTC](https://community.brain-map.org/t/deep-generative-mapping-on-your-own-machine/5049 "2026-08-25T16:51:35Z")
Hi, Great tool! If I want to use the Deep Generative Mapping algorithm locally, how would I go about it? It looks like the current version for cell type mapper on github only supports “Correlation Mapping” and “Hierarc… --- ## [New Customization Options Now Available in ABC Atlas](https://community.brain-map.org/t/new-customization-options-now-available-in-abc-atlas/4891)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 3\ **Last updated:** [August 25, 2026, 1:42pm UTC](https://community.brain-map.org/t/new-customization-options-now-available-in-abc-atlas/4891 "2026-08-25T13:42:13Z")
The ABC Atlas has been updated with a host of new options for customizing your views. These changes came directly as a result of suggestions from scientists and there’s more on the way. Thank you for your feedback and ke… --- ## [High schooler interested in music-induced neuroplasticity looking for where to start](https://community.brain-map.org/t/high-schooler-interested-in-music-induced-neuroplasticity-looking-for-where-to-start/5005)
**Author:** [@samjoonlee](https://community.brain-map.org/u/samjoonlee)\ **Replies:** 1\ **Last updated:** [August 19, 2026, 7:46pm UTC](https://community.brain-map.org/t/high-schooler-interested-in-music-induced-neuroplasticity-looking-for-where-to-start/5005 "2026-08-19T19:46:55Z")
Hello everyone My name is Samuel Lee, and I am a high school student residing in Lexington, MA, attending Lexington High School and particularly drawn to cognitive and computational neuroscience. I am fascinated by the … --- ## [Allen scSeq Dataset ](https://community.brain-map.org/t/allen-scseq-dataset/5044)
**Author:** [@BWalters](https://community.brain-map.org/u/BWalters)\ **Replies:** 1\ **Last updated:** [August 13, 2026, 5:36pm UTC](https://community.brain-map.org/t/allen-scseq-dataset/5044 "2026-08-13T17:36:50Z")
Hello, I am a graduate student in a circadian neuroscience lab and we have been using the single cell adult mouse brain public datasets for some preliminary/exploratory analyses. I was hoping to get some information abou… --- ## [Question about MERFISH Imputation Within-Cluster KNN Matching](https://community.brain-map.org/t/question-about-merfish-imputation-within-cluster-knn-matching/5003)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 1\ **Last updated:** [August 12, 2026, 4:54am UTC](https://community.brain-map.org/t/question-about-merfish-imputation-within-cluster-knn-matching/5003 "2026-08-12T04:54:29Z")
Hello, Thank you very much for providing the ABC Atlas and the detailed documentation. I think I understand the overall workflow of the MERFISH imputation process. My understanding is: MERFISH cells are first mapped … --- ## [Request for information on pre-euthanasia handling of mice used in the MERFISH dataset](https://community.brain-map.org/t/request-for-information-on-pre-euthanasia-handling-of-mice-used-in-the-merfish-dataset/5034)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 1\ **Last updated:** [August 11, 2026, 3:58pm UTC](https://community.brain-map.org/t/request-for-information-on-pre-euthanasia-handling-of-mice-used-in-the-merfish-dataset/5034 "2026-08-11T15:58:03Z")
Dear Allen Institute team, I am analyzing spatial expression patterns of immediate-early genes (IEGs) in the olfactory tubercle using the adult mouse whole-brain MERFISH dataset. Because IEG expression can change rapidl… --- ## [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… --- ## [Issue Downloading Microarray Dataset for Donor H0351.1015](https://community.brain-map.org/t/issue-downloading-microarray-dataset-for-donor-h0351-1015/5011)
**Author:** [@Maria.YH.Lee](https://community.brain-map.org/u/Maria.YH.Lee)\ **Replies:** 7\ **Last updated:** [August 7, 2026, 4:16pm UTC](https://community.brain-map.org/t/issue-downloading-microarray-dataset-for-donor-h0351-1015/5011 "2026-08-07T16:16:27Z")
I am trying to download the microarray dataset containing the gene expression values for donor H0351.1015, but I receive the following message: “The page you were looking for doesn’t exist. You may have mistyped the ad… --- ## [Donor mapping for MERFISH MEC/HPF specimens](https://community.brain-map.org/t/donor-mapping-for-merfish-mec-hpf-specimens/5020)
**Author:** [@TamaraV](https://community.brain-map.org/u/TamaraV)\ **Replies:** 4\ **Last updated:** [August 4, 2026, 8:44pm UTC](https://community.brain-map.org/t/donor-mapping-for-merfish-mec-hpf-specimens/5020 "2026-08-04T20:44:53Z")
I’m working with two SEA-AD MERFISH files from the spatial-transcriptomics bucket: medial-entorhinal-cortex/combined\_anndata\_object/1444201261\_MEC\_mapped.h5ad andhippocampus/combined\_anndata\_object/1444211893\_HPF\_mapped.… --- ## [Thank You for Making Cross-Border Neuroscience Possible with the Allen Brain Cell Atlas](https://community.brain-map.org/t/thank-you-for-making-cross-border-neuroscience-possible-with-the-allen-brain-cell-atlas/5036)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 2\ **Last updated:** [August 1, 2026, 2:43am UTC](https://community.brain-map.org/t/thank-you-for-making-cross-border-neuroscience-possible-with-the-allen-brain-cell-atlas/5036 "2026-08-01T02:43:17Z")
Dear Allen Institute team and everyone involved in the Allen Brain Cell Atlas I am a researcher at the University of Fukui in Japan, and I would like to express my sincere gratitude to everyone who contributed to the de… --- ## [Questions about Allen Mouse Brain Connectivity Atlas projection and injection data](https://community.brain-map.org/t/questions-about-allen-mouse-brain-connectivity-atlas-projection-and-injection-data/5000)
**Author:** [@omar341](https://community.brain-map.org/u/omar341)\ **Replies:** 1\ **Last updated:** [July 30, 2026, 5:38pm UTC](https://community.brain-map.org/t/questions-about-allen-mouse-brain-connectivity-atlas-projection-and-injection-data/5000 "2026-07-30T17:38:49Z")
Hi, I am a PhD student working on stochastic connectome-based modeling of pathological particle propagation in the mouse brain. I am using the Allen Mouse Brain Connectivity Atlas, especially the projection dataset from … --- ## [(SEA-AD) Donors and Samples](https://community.brain-map.org/t/sea-ad-donors-and-samples/4669)
**Author:** [@Victhagas](https://community.brain-map.org/u/Victhagas)\ **Replies:** 6\ **Last updated:** [July 26, 2026, 10:07pm UTC](https://community.brain-map.org/t/sea-ad-donors-and-samples/4669 "2026-07-26T22:07:05Z")
Hi guys, I was performing DEG analysis on the SEA-AD data and got confused about two things: When we access the AWS S3 Explorer, we can get the donor data, there are around 84 .h5ad files. I checked, and many of them… --- ## [Nomalized microarray datasets download](https://community.brain-map.org/t/nomalized-microarray-datasets-download/5028)
**Author:** [@maomao](https://community.brain-map.org/u/maomao)\ **Replies:** 1\ **Last updated:** [July 21, 2026, 5:59pm UTC](https://community.brain-map.org/t/nomalized-microarray-datasets-download/5028 "2026-07-21T17:59:20Z")
when I clicked the H0351.1015 to get normalized\_microarray\_donor\_15496，the websites showed“the page you were looking for doesnt exist”.Is it an error？ or information Lost？i really need this document，please fix that. --- ## [Call for Volunteers](https://community.brain-map.org/t/call-for-volunteers/5009)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [July 9, 2026, 5:09pm UTC](https://community.brain-map.org/t/call-for-volunteers/5009 "2026-07-09T17:09:09Z")
We’re conducting a usability study of the Allen Institute ABC Atlas and are looking for scientists willing to spend approximately 60 minutes with us. Sessions can be completed on your own schedule from August 10 through … [Next page](https://community.brain-map.org/latest.md?page=1)