# General **URL:** https://community.brain-map.org/c/general/1.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 --- ## [Variables in the XML file (brain connectivity)](https://community.brain-map.org/t/variables-in-the-xml-file-brain-connectivity/4392)
**Author:** [@rokkha](https://community.brain-map.org/u/rokkha)\ **Replies:** 2\ **Last updated:** [March 27, 2026, 3:53pm UTC](https://community.brain-map.org/t/variables-in-the-xml-file-brain-connectivity/4392 "2026-03-27T15:53:45Z")
Hi, The projection volume graph shows the amount of connectivity received by target structures from the origin (injection site). Near the bottom, the data is also available as XML. I am having trouble mapping the variab… --- ## [Spatial mapping of GABAergic neurons](https://community.brain-map.org/t/spatial-mapping-of-gabaergic-neurons/4869)
**Author:** [@realshyshy](https://community.brain-map.org/u/realshyshy)\ **Replies:** 1\ **Last updated:** [March 27, 2026, 3:47pm UTC](https://community.brain-map.org/t/spatial-mapping-of-gabaergic-neurons/4869 "2026-03-27T15:47:33Z")
How can I utilize Allen Brain Atlas data to annotate and map GABAergic neurons identified in my single-nucleus RNA-seq dataset to specific brain subregions? --- ## [API reference page is unreachable](https://community.brain-map.org/t/api-reference-page-is-unreachable/4609)
**Author:** [@maflot](https://community.brain-map.org/u/maflot)\ **Replies:** 2\ **Last updated:** [February 25, 2026, 12:42pm UTC](https://community.brain-map.org/t/api-reference-page-is-unreachable/4609 "2026-02-25T12:42:54Z")
The link to the API reference on Is showing me that this is private or non existent. https://community.brain-map.org/confluence/display/DataAPI/Home Is there a way to get access to the API and to the reference for t… --- ## [Scrattch.patchseq - patching from multiple classess](https://community.brain-map.org/t/scrattch-patchseq-patching-from-multiple-classess/4854)
**Author:** [@marsdenl](https://community.brain-map.org/u/marsdenl)\ **Replies:** 2\ **Last updated:** [February 23, 2026, 2:08am UTC](https://community.brain-map.org/t/scrattch-patchseq-patching-from-multiple-classess/4854 "2026-02-23T02:08:57Z")
Hey there, First of all, the patchseq tool has been an absolute life saver so thanks for making it accessible. I was wondering if there was a good way to calculate the NMS score for multiple ‘ON classes’ at once? For i… --- ## [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… --- ## [Human GPi subset question](https://community.brain-map.org/t/human-gpi-subset-question/4833)
**Author:** [@gchatt](https://community.brain-map.org/u/gchatt)\ **Replies:** 0\ **Last updated:** [January 22, 2026, 3:24am UTC](https://community.brain-map.org/t/human-gpi-subset-question/4833 "2026-01-22T03:24:23Z")
Hi, please feel free to delete this post if it is inappropriate. I just received a reviewer comment that ‘many studies’ have shown there is no PVALB+/GAD+/LYPD1+ subset of neurons in the GPi in humans. I have analyzed t… --- ## [Mapmycells reliability](https://community.brain-map.org/t/mapmycells-reliability/4830)
**Author:** [@Sim](https://community.brain-map.org/u/Sim)\ **Replies:** 1\ **Last updated:** [January 20, 2026, 10:15pm UTC](https://community.brain-map.org/t/mapmycells-reliability/4830 "2026-01-20T22:15:53Z")
Hi, Thank you for the brilliant tool with mapmycells! I was wondering what the recommendations are for ensuring reliability? I have been looking at the probability etc and have found that expectedly cells with a lower … --- ## [Your search could not be completed - \[Object - object\]](https://community.brain-map.org/t/your-search-could-not-be-completed-object-object/4828)
**Author:** [@Josefazaldivar](https://community.brain-map.org/u/Josefazaldivar)\ **Replies:** 2\ **Last updated:** [January 20, 2026, 4:42pm UTC](https://community.brain-map.org/t/your-search-could-not-be-completed-object-object/4828 "2026-01-20T16:42:34Z")
Hello, I have been trying since yesterday to use the microarray data in the human brain atlas and this message keeps poping up. Is anyone experiencing the same problem? --- ## [GPi = EPN in mouse brain atlas?](https://community.brain-map.org/t/gpi-epn-in-mouse-brain-atlas/4814)
**Author:** [@LivPhD](https://community.brain-map.org/u/LivPhD)\ **Replies:** 2\ **Last updated:** [January 19, 2026, 10:17pm UTC](https://community.brain-map.org/t/gpi-epn-in-mouse-brain-atlas/4814 "2026-01-19T22:17:46Z")
Hi everyone, Just wanted to confirm that the GPi labelled on the adult mouse brain atlas is in fact the entopeduncular nucleus (EP/EPN)? I know they’re functional analogues and the literature shows histology in about th… --- ## [For the Gabitto et al manuscript, was any sort of ambient RNA detection performed for the query MTG?](https://community.brain-map.org/t/for-the-gabitto-et-al-manuscript-was-any-sort-of-ambient-rna-detection-performed-for-the-query-mtg/4804)
**Author:** [@ashaypatel](https://community.brain-map.org/u/ashaypatel)\ **Replies:** 2\ **Last updated:** [January 16, 2026, 10:30pm UTC](https://community.brain-map.org/t/for-the-gabitto-et-al-manuscript-was-any-sort-of-ambient-rna-detection-performed-for-the-query-mtg/4804 "2026-01-16T22:30:57Z")
For the Gabitto et al manuscript, was any sort of ambient RNA detection performed for the query MTG? Thanks, --- ## [Details about developmental transcriptome (human)](https://community.brain-map.org/t/details-about-developmental-transcriptome-human/4825)
**Author:** [@Anna](https://community.brain-map.org/u/Anna)\ **Replies:** 1\ **Last updated:** [January 12, 2026, 4:38pm UTC](https://community.brain-map.org/t/details-about-developmental-transcriptome-human/4825 "2026-01-12T16:38:48Z")
Dear all, I have downloaded the data of a specific gene of interest as I would like to visualize its expression overtime prenatally. In the annotation of the brain areas I see different classifications: either “top level… --- ## [I am seeing a cluster in the query that is not alligning with ref (SEA-AD snRNAseq MTG) (Part 2)](https://community.brain-map.org/t/i-am-seeing-a-cluster-in-the-query-that-is-not-alligning-with-ref-sea-ad-snrnaseq-mtg-part-2/4811)
**Author:** [@ashaypatel](https://community.brain-map.org/u/ashaypatel)\ **Replies:** 1\ **Last updated:** [January 12, 2026, 4:29pm UTC](https://community.brain-map.org/t/i-am-seeing-a-cluster-in-the-query-that-is-not-alligning-with-ref-sea-ad-snrnaseq-mtg-part-2/4811 "2026-01-12T16:29:00Z")
I created a query data set using SEA-AD snRNAseq MTG data from the raw fastqs at sage Synape (with clinical consensus diagnosis of Alzheimers disease and Control). I ran cell ranger (with introns) and perfomed QC. The re… --- ## [The meaning of the y/z value of the electrodes in the Allen neuropixel dataset](https://community.brain-map.org/t/the-meaning-of-the-y-z-value-of-the-electrodes-in-the-allen-neuropixel-dataset/4809)
**Author:** [@maryamgh](https://community.brain-map.org/u/maryamgh)\ **Replies:** 1\ **Last updated:** [December 18, 2025, 1:12am UTC](https://community.brain-map.org/t/the-meaning-of-the-y-z-value-of-the-electrodes-in-the-allen-neuropixel-dataset/4809 "2025-12-18T01:12:01Z")
Hi, I have a question about the y/z value of the electrodes in the Allen neuropixel dataset; Do they show the depth with respect to the pia? What does positive and negative values mean? I want to find the layer of each c… --- ## [Group Plot for Basal Ganglia cell types](https://community.brain-map.org/t/group-plot-for-basal-ganglia-cell-types/4791)
**Author:** [@Harker](https://community.brain-map.org/u/Harker)\ **Replies:** 3\ **Last updated:** [December 12, 2025, 6:04pm UTC](https://community.brain-map.org/t/group-plot-for-basal-ganglia-cell-types/4791 "2025-12-12T18:04:41Z")
How can I get a “Group Plot” like the ones I used to get from http:/celltypes.brain-map.org/rnaseq/human/mtg for Basal Ganglia cell types? --- ## [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… --- ## [Accessing full resolution region segmentations for Mouse, P56, Sagittal atlas](https://community.brain-map.org/t/accessing-full-resolution-region-segmentations-for-mouse-p56-sagittal-atlas/4788)
**Author:** [@mukund](https://community.brain-map.org/u/mukund)\ **Replies:** 2\ **Last updated:** [December 5, 2025, 3:21pm UTC](https://community.brain-map.org/t/accessing-full-resolution-region-segmentations-for-mouse-p56-sagittal-atlas/4788 "2025-12-05T15:21:27Z")
Hi, I’m trying to download region segmentations for the Mouse, P56, Sagittal atlas using the Allen image download API . However, the images downloaded via the API seem to have region segmentations at a much lower detail … --- ## [Color duplicates in reference atlas images](https://community.brain-map.org/t/color-duplicates-in-reference-atlas-images/4720)
**Author:** [@julianrode](https://community.brain-map.org/u/julianrode)\ **Replies:** 4\ **Last updated:** [December 1, 2025, 10:36pm UTC](https://community.brain-map.org/t/color-duplicates-in-reference-atlas-images/4720 "2025-12-01T22:36:27Z")
Hi everyone! I am working on implementing atlas registration in ImageJ, and have used the color of the brain regions together with the color\_hex\_triplet from the structure ontology .csv file: http://api.brain-map.org/… --- ## [Allen mouse brain connectivity atlas has been down for the last few days](https://community.brain-map.org/t/allen-mouse-brain-connectivity-atlas-has-been-down-for-the-last-few-days/4764)
**Author:** [@kbw](https://community.brain-map.org/u/kbw)\ **Replies:** 5\ **Last updated:** [November 24, 2025, 10:37pm UTC](https://community.brain-map.org/t/allen-mouse-brain-connectivity-atlas-has-been-down-for-the-last-few-days/4764 "2025-11-24T22:37:43Z")
Hi, It seems that Allen mouse brain connectivity atlas has been down for the last few days. Could anyone fix this? Thank you! --- ## [Eye tracking camera components](https://community.brain-map.org/t/eye-tracking-camera-components/4766)
**Author:** [@sonali.sriranga](https://community.brain-map.org/u/sonali.sriranga)\ **Replies:** 0\ **Last updated:** [November 14, 2025, 2:26pm UTC](https://community.brain-map.org/t/eye-tracking-camera-components/4766 "2025-11-14T14:26:53Z")
Hi, I’m trying to setup the eye tracking camera as described in the Allen White Paper Visual Behaviour 2P and I was wondering what components were used to mount Semrock FF01-850/10-25 bandpass filter onto the camera? Th… --- ## [Code of CPS (Continuous Pseudoprogression Score)](https://community.brain-map.org/t/code-of-cps-continuous-pseudoprogression-score/4743)
**Author:** [@xiefanfan](https://community.brain-map.org/u/xiefanfan)\ **Replies:** 0\ **Last updated:** [November 5, 2025, 4:45pm UTC](https://community.brain-map.org/t/code-of-cps-continuous-pseudoprogression-score/4743 "2025-11-05T16:45:20Z")
Hello @kyle.travaglini Can I request the code for calculating the CPS (Continuous Pseudoprogression Score) please？ Thank you for your share! --- ## [In Situ Hybridization (ISH) sample preparation](https://community.brain-map.org/t/in-situ-hybridization-ish-sample-preparation/4734)
**Author:** [@biahaoyama](https://community.brain-map.org/u/biahaoyama)\ **Replies:** 1\ **Last updated:** [October 30, 2025, 11:51pm UTC](https://community.brain-map.org/t/in-situ-hybridization-ish-sample-preparation/4734 "2025-10-30T23:51:10Z")
Hi, How did you prepare the samples for ISH of human tissue? Was the tissue frozen or fixed and paraffin-embedded? Thanks --- ## [Mouse Connectivity Projection Density Units](https://community.brain-map.org/t/mouse-connectivity-projection-density-units/1850)
**Author:** [@kavkon](https://community.brain-map.org/u/kavkon)\ **Replies:** 2\ **Last updated:** [October 30, 2025, 8:02pm UTC](https://community.brain-map.org/t/mouse-connectivity-projection-density-units/1850 "2025-10-30T20:02:31Z")
I would like to use the data from the injections in the mouse brain connectivity tool, but I am having a slight issue understanding it. When viewing the data, I have the option to switch the data from “Projection Volume… --- ## [Duplicated ISH data for certain genes in mouse brain atlas](https://community.brain-map.org/t/duplicated-ish-data-for-certain-genes-in-mouse-brain-atlas/1709)
**Author:** [@LGar](https://community.brain-map.org/u/LGar)\ **Replies:** 1\ **Last updated:** [October 24, 2025, 6:20pm UTC](https://community.brain-map.org/t/duplicated-ish-data-for-certain-genes-in-mouse-brain-atlas/1709 "2025-10-24T18:20:29Z")
Hi, I couldn’t find the answer already in the forum but can you tell me why there is duplicated ISH data for certain genes in the mouse brain atlas? Is it a repeat analysis where the first was not successful? Thanks, … --- ## [H5ad File Characteristics](https://community.brain-map.org/t/h5ad-file-characteristics/3595)
**Author:** [@karte](https://community.brain-map.org/u/karte)\ **Replies:** 4\ **Last updated:** [September 16, 2025, 2:48am UTC](https://community.brain-map.org/t/h5ad-file-characteristics/3595 "2025-09-16T02:48:41Z")
Hello, I’m currently working with the SEAAD\_MTG\_RNAseq\_final-nuclei.2024-02-13.h5ad dataset and it’s my first time working with RNAseq data, so please excuse the simplicity of the questions. I was just wondering a few th… --- ## [Hello everyone, I would like to ask how to download or generate the dorsal projection of the mouse universal coordinate frame, like the one below](https://community.brain-map.org/t/hello-everyone-i-would-like-to-ask-how-to-download-or-generate-the-dorsal-projection-of-the-mouse-universal-coordinate-frame-like-the-one-below/4591)
**Author:** [@lyc](https://community.brain-map.org/u/lyc)\ **Replies:** 1\ **Last updated:** [July 29, 2025, 7:05pm UTC](https://community.brain-map.org/t/hello-everyone-i-would-like-to-ask-how-to-download-or-generate-the-dorsal-projection-of-the-mouse-universal-coordinate-frame-like-the-one-below/4591 "2025-07-29T19:05:07Z")
Hello everyone, I would like to ask how to download or generate the dorsal projection brain area data of the mouse general coordinate framework, roughly like the picture below, for subsequent ROI data analysis? --- ## [Clarifying how MMC reclassifies Allen reference cells](https://community.brain-map.org/t/clarifying-how-mmc-reclassifies-allen-reference-cells/4569)
**Author:** [@RebecaO](https://community.brain-map.org/u/RebecaO)\ **Replies:** 4\ **Last updated:** [July 29, 2025, 7:03pm UTC](https://community.brain-map.org/t/clarifying-how-mmc-reclassifies-allen-reference-cells/4569 "2025-07-29T19:03:37Z")
Hi everyone, I’ve been working with the Allen reference dataset (Whole Cortex & Hippocampus - 10x Genomics (2020) with 10x-SMART-seq taxonomy \[2021\]) and using MapMyCells (MMC) to classify both my own snRNA-seq samples … --- ## [Metadata/Publication for SMART-Seq v4 DFC M1C Dataset](https://community.brain-map.org/t/metadata-publication-for-smart-seq-v4-dfc-m1c-dataset/4553)
**Author:** [@berilerdogdu](https://community.brain-map.org/u/berilerdogdu)\ **Replies:** 1\ **Last updated:** [July 29, 2025, 3:18pm UTC](https://community.brain-map.org/t/metadata-publication-for-smart-seq-v4-dfc-m1c-dataset/4553 "2025-07-29T15:18:29Z")
Hello! I recently came across a dataset uploaded by your group to the Brain Knowledge Platform (nemo:dat-72qka5t), available at: This dataset contains SMART-Seq v4 RNA-Seq reads from human cortical areas M1C and DFC,… --- ## [Issue selecting cells and exporting data from the Brain Knowledge Platform](https://community.brain-map.org/t/issue-selecting-cells-and-exporting-data-from-the-brain-knowledge-platform/4535)
**Author:** [@Madhurima](https://community.brain-map.org/u/Madhurima)\ **Replies:** 5\ **Last updated:** [July 18, 2025, 9:26am UTC](https://community.brain-map.org/t/issue-selecting-cells-and-exporting-data-from-the-brain-knowledge-platform/4535 "2025-07-18T09:26:08Z")
I have been using the Brain Knowledge Platform to look at expression data across a few of the available studies, and recently (the last few months) when I select a population of cells in a brain region using the dashed r… --- ## [Request for sample and read mapping QC metadata](https://community.brain-map.org/t/request-for-sample-and-read-mapping-qc-metadata/4477)
**Author:** [@xyaous](https://community.brain-map.org/u/xyaous)\ **Replies:** 7\ **Last updated:** [June 21, 2025, 2:34am UTC](https://community.brain-map.org/t/request-for-sample-and-read-mapping-qc-metadata/4477 "2025-06-21T02:34:37Z")
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 … --- ## [How to find specific cell types that express a certain gene?](https://community.brain-map.org/t/how-to-find-specific-cell-types-that-express-a-certain-gene/4446)
**Author:** [@ramses02](https://community.brain-map.org/u/ramses02)\ **Replies:** 2\ **Last updated:** [June 10, 2025, 4:32pm UTC](https://community.brain-map.org/t/how-to-find-specific-cell-types-that-express-a-certain-gene/4446 "2025-06-10T16:32:25Z")
Hi everyone! My name is Ramsi and I am looking at the function of Opsin 3, a non-visual opsin (GPCR), in the brain. Specifically, I am looking to find cells in the hippocampus, cortex, and thalamus that express OPN3. Fro… [Previous page](https://community.brain-map.org/c/general/1.md) [Next page](https://community.brain-map.org/c/general/1.md?page=2)