# General **URL:** https://community.brain-map.org/c/general/1.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… --- ## [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 … --- ## [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… --- ## [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 … --- ## [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… --- ## [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 … --- ## [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… --- ## [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… --- ## [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/5007)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [July 8, 2026, 5:00pm UTC](https://community.brain-map.org/t/call-for-volunteers/5007 "2026-07-08T17:00:51Z")
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 … --- ## [Units of Coordinates in the ABC Atlas](https://community.brain-map.org/t/units-of-coordinates-in-the-abc-atlas/4997)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 1\ **Last updated:** [July 2, 2026, 5:15pm UTC](https://community.brain-map.org/t/units-of-coordinates-in-the-abc-atlas/4997 "2026-07-02T17:15:24Z")
What are the units used for the x and y coordinates in the MERFISH with imputed gene dataset? --- ## [Left–Right Orientation of ABC Atlas Sections](https://community.brain-map.org/t/left-right-orientation-of-abc-atlas-sections/4998)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 0\ **Last updated:** [July 2, 2026, 1:43am UTC](https://community.brain-map.org/t/left-right-orientation-of-abc-atlas-sections/4998 "2026-07-02T01:43:41Z")
I would like to confirm the left–right orientation of the coronal sections in the ABC Atlas. For the x coordinate, does a smaller x value correspond to the left hemisphere or the right hemisphere? Thank you for your help… --- ## [Amyloid plaque distance from cell](https://community.brain-map.org/t/amyloid-plaque-distance-from-cell/4992)
**Author:** [@Rajesh](https://community.brain-map.org/u/Rajesh)\ **Replies:** 2\ **Last updated:** [June 30, 2026, 8:05am UTC](https://community.brain-map.org/t/amyloid-plaque-distance-from-cell/4992 "2026-06-30T08:05:01Z")
Dear all, I have the global positioning data for each cell from the spatial transcriptomics data made publicly available publicly via AWS by the SEA-AD consortium. However, I am unable to access the distance of each cell… --- ## [Unable to access the technical whitepaper on the experimental design, data acquisition, and informatics methods from https://allensdk.readthedocs.io/en/latest/visual\_coding\_neuropixels.html](https://community.brain-map.org/t/unable-to-access-the-technical-whitepaper-on-the-experimental-design-data-acquisition-and-informatics-methods-from-https-allensdk-readthedocs-io-en-latest-visual-coding-neuropixels-html/4985)
**Author:** [@indrag49](https://community.brain-map.org/u/indrag49)\ **Replies:** 6\ **Last updated:** [June 15, 2026, 3:23pm UTC](https://community.brain-map.org/t/unable-to-access-the-technical-whitepaper-on-the-experimental-design-data-acquisition-and-informatics-methods-from-https-allensdk-readthedocs-io-en-latest-visual-coding-neuropixels-html/4985 "2026-06-15T15:23:19Z")
The link to access the technical white paper on the experimental design, data acquisition, and informatics methods from the page Visual Coding – Neuropixels — Allen SDK dev documentation looks broken. I am currently writ… --- ## [Is mouse ISH atlas down?](https://community.brain-map.org/t/is-mouse-ish-atlas-down/4973)
**Author:** [@Zhihui](https://community.brain-map.org/u/Zhihui)\ **Replies:** 1\ **Last updated:** [June 8, 2026, 8:30pm UTC](https://community.brain-map.org/t/is-mouse-ish-atlas-down/4973 "2026-06-08T20:30:05Z")
Cant access it. Every time I tried to search a gene, it shows “Error in query: , Can’t connect to MySQL server on ‘127.0.0.1’ (111)”. Does anyone know what I should do? --- ## [ID mapping between SEA-AD and ACT](https://community.brain-map.org/t/id-mapping-between-sea-ad-and-act/4907)
**Author:** [@qwang178](https://community.brain-map.org/u/qwang178)\ **Replies:** 1\ **Last updated:** [June 6, 2026, 1:48pm UTC](https://community.brain-map.org/t/id-mapping-between-sea-ad-and-act/4907 "2026-06-06T13:48:16Z")
Hi there, I am wondering if there is any ID mapping information available for the SEA-AD snRNAseq data and the original ACT study? Specifically, we are trying to run eQTL analysis and would like to link the transcriptom… --- ## [Question about meshes](https://community.brain-map.org/t/question-about-meshes/4916)
**Author:** [@scruffy](https://community.brain-map.org/u/scruffy)\ **Replies:** 4\ **Last updated:** [June 4, 2026, 12:35am UTC](https://community.brain-map.org/t/question-about-meshes/4916 "2026-06-04T00:35:36Z")
Greetings, I’m new to Allen and the forum but have been engaged with neuroscience for a very long time. I’m interested in doing some finite element work and would like to inquire about the availability and condition of a… --- ## [Is there a mapping of neural mitochondria?](https://community.brain-map.org/t/is-there-a-mapping-of-neural-mitochondria/4922)
**Author:** [@scruffy](https://community.brain-map.org/u/scruffy)\ **Replies:** 1\ **Last updated:** [June 3, 2026, 11:16pm UTC](https://community.brain-map.org/t/is-there-a-mapping-of-neural-mitochondria/4922 "2026-06-03T23:16:51Z")
Especially interested in hippocampus CA2. Yet another area where meshes can be intensely helpful. Has anyone actually meshed an entire neuron with all its parts? --- ## [How should the effective sample size (n) be considered?](https://community.brain-map.org/t/how-should-the-effective-sample-size-n-be-considered/4888)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 1\ **Last updated:** [April 29, 2026, 10:58pm UTC](https://community.brain-map.org/t/how-should-the-effective-sample-size-n-be-considered/4888 "2026-04-29T22:58:58Z")
I have a question regarding the interpretation of sample size when using the imputed MERFISH data in the ABC Atlas. If one uses the imputed dataset for analysis and publication, how should the effective sample size (n) … --- ## [Coordinate system in ABC atlas log2 imputed MERFISH dataset](https://community.brain-map.org/t/coordinate-system-in-abc-atlas-log2-imputed-merfish-dataset/4887)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 0\ **Last updated:** [April 23, 2026, 7:38am UTC](https://community.brain-map.org/t/coordinate-system-in-abc-atlas-log2-imputed-merfish-dataset/4887 "2026-04-23T07:38:14Z")
I have a question regarding the coordinate system used in the ABC atlas log2 imputed MERFISH dataset Specifically, for the x-coordinate, could you clarify whether smaller values correspond to the left or the right side … --- ## [Repeated Recording from the same specimen Visual Coding Neuropixels](https://community.brain-map.org/t/repeated-recording-from-the-same-specimen-visual-coding-neuropixels/4882)
**Author:** [@Leofierus](https://community.brain-map.org/u/Leofierus)\ **Replies:** 1\ **Last updated:** [April 15, 2026, 10:33pm UTC](https://community.brain-map.org/t/repeated-recording-from-the-same-specimen-visual-coding-neuropixels/4882 "2026-04-15T22:33:02Z")
Hi! Are there any lfp recordings from the same specimen taken some days apart in the data? I could not find any in the sessions.csv from the cache but making sure. --- ## [Spatial Merfish data of ABC atlas](https://community.brain-map.org/t/spatial-merfish-data-of-abc-atlas/4878)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 2\ **Last updated:** [April 10, 2026, 3:56pm UTC](https://community.brain-map.org/t/spatial-merfish-data-of-abc-atlas/4878 "2026-04-10T15:56:26Z")
I am working with the MERFISH dataset (C57BL6J-638850 imputed gene) from the Allen Brain Cell Atlas and have a question regarding how to correctly link spatial and gene expression data. I understand that: The imputed… --- ## [Histogram for a specific gene on ABC atlas](https://community.brain-map.org/t/histogram-for-a-specific-gene-on-abc-atlas/4877)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 2\ **Last updated:** [April 10, 2026, 5:09am UTC](https://community.brain-map.org/t/histogram-for-a-specific-gene-on-abc-atlas/4877 "2026-04-10T05:09:36Z")
Dear Allen Brain Institute team I am currently analyzing gene expression data from the Allen Brain Cell Atlas and have a question regarding the histograms provided for individual genes. I noticed that the bin widths in… --- ## [MICrONS with CCF](https://community.brain-map.org/t/microns-with-ccf/4866)
**Author:** [@jyy20422](https://community.brain-map.org/u/jyy20422)\ **Replies:** 1\ **Last updated:** [April 6, 2026, 4:36pm UTC](https://community.brain-map.org/t/microns-with-ccf/4866 "2026-04-06T16:36:47Z")
Hello All, is there a way to obtain the CCF coordinates for the neurons in the MICrONS dataset or register the dataset to the CCF atlas? Thank you! --- ## [Cheat sheet for annotation?](https://community.brain-map.org/t/cheat-sheet-for-annotation/3488)
**Author:** [@Spirometra](https://community.brain-map.org/u/Spirometra)\ **Replies:** 7\ **Last updated:** [April 2, 2026, 11:47pm UTC](https://community.brain-map.org/t/cheat-sheet-for-annotation/3488 "2026-04-02T23:47:58Z")
Hi Brainy community! I am looking for a cheat sheet for the cell class and anatomical acronyms used in the atlases (both human and mouse) under cell properties. I can make guesses as to what a lot of them are, but I wou… [Next page](https://community.brain-map.org/c/general/1.md?page=1)