# How To **URL:** https://community.brain-map.org/c/how-to/15.md?page=2 [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:** 3 --- ## [Hello everyone, I am trying to map my entire mouse brain MERFISH sections of P4 & P7 to the Allen Brain Atlas and annotate the brain regions. Could anyone clarify the exact input data required for this process?](https://community.brain-map.org/t/hello-everyone-i-am-trying-to-map-my-entire-mouse-brain-merfish-sections-of-p4-p7-to-the-allen-brain-atlas-and-annotate-the-brain-regions-could-anyone-clarify-the-exact-input-data-required-for-this-process/3941)
**Author:** [@kulansam](https://community.brain-map.org/u/kulansam)\ **Replies:** 8\ **Last updated:** [August 13, 2025, 3:55pm UTC](https://community.brain-map.org/t/hello-everyone-i-am-trying-to-map-my-entire-mouse-brain-merfish-sections-of-p4-p7-to-the-allen-brain-atlas-and-annotate-the-brain-regions-could-anyone-clarify-the-exact-input-data-required-for-this-process/3941 "2025-08-13T15:55:21Z")
I have gone through the tutorial at MERFISH whole brain spatial transcriptomics (part 1) — Allen Brain Cell Atlas - Data Access. I understand that the input data should include x, y, and z coordinates. Could you clarify … --- ## [Measurements in mouse brain atlas](https://community.brain-map.org/t/measurements-in-mouse-brain-atlas/4543)
**Author:** [@etn5337](https://community.brain-map.org/u/etn5337)\ **Replies:** 1\ **Last updated:** [August 11, 2025, 5:09pm UTC](https://community.brain-map.org/t/measurements-in-mouse-brain-atlas/4543 "2025-08-11T17:09:51Z")
Hi! Apologies if this is a very simple thing to do. I’m hoping to find measurements of the distance of layer 5 from the pial surface as well as the pial surface area in primary somatosensory, visual and auditory cortices… --- ## [How to get white matter tract anisotropy](https://community.brain-map.org/t/how-to-get-white-matter-tract-anisotropy/4563)
**Author:** [@bricoyle](https://community.brain-map.org/u/bricoyle)\ **Replies:** 1\ **Last updated:** [August 11, 2025, 3:37pm UTC](https://community.brain-map.org/t/how-to-get-white-matter-tract-anisotropy/4563 "2025-08-11T15:37:46Z")
The Allen Brain Atlas contains valuable white matter tract data. How do we obtain white matter anisotropy, showing the direction of bundled axons? --- ## [Scientists search projects using own search terms via Text Search in Brain Knowledge Platform’s Data Catalog](https://community.brain-map.org/t/scientists-search-projects-using-own-search-terms-via-text-search-in-brain-knowledge-platform-s-data-catalog/4607)
**Author:** [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Replies:** 0\ **Last updated:** [August 4, 2025, 8:59pm UTC](https://community.brain-map.org/t/scientists-search-projects-using-own-search-terms-via-text-search-in-brain-knowledge-platform-s-data-catalog/4607 "2025-08-04T20:59:52Z")
The Data Catalog’s new Text Search empowers scientists to search for relevant resources with their own search terms. Text search in Data Catalog Access the Data Catalog’s text search field at https://knowledge.brain-map… --- ## [API for Allen Developing Mouse Brain Atlas](https://community.brain-map.org/t/api-for-allen-developing-mouse-brain-atlas/2855)
**Author:** [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Replies:** 5\ **Last updated:** [August 4, 2025, 7:07pm UTC](https://community.brain-map.org/t/api-for-allen-developing-mouse-brain-atlas/2855 "2025-08-04T19:07:37Z")
Experimental Overview and Metadata Informatics Data Processing 3-D Reference Models Image Alignment Expression Detection Expression Gridding Structure Unionization Expression Grid Search Service Expert Manual Annotat… --- ## [Downloading an Image](https://community.brain-map.org/t/downloading-an-image/2865)
**Author:** [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Replies:** 3\ **Last updated:** [July 28, 2025, 10:36pm UTC](https://community.brain-map.org/t/downloading-an-image/2865 "2025-07-28T22:36:20Z")
Image Download Service AtlasImage Download Service Download whole or partial two-dimensional images from the Allen Institute with the Image and AtlasImage Download Services. Image Download Service The Image download … --- ## [Normalisation protocol and cell types](https://community.brain-map.org/t/normalisation-protocol-and-cell-types/4589)
**Author:** [@HG\_58828](https://community.brain-map.org/u/HG_58828)\ **Replies:** 2\ **Last updated:** [July 28, 2025, 6:06pm UTC](https://community.brain-map.org/t/normalisation-protocol-and-cell-types/4589 "2025-07-28T18:06:54Z")
I am quite new to RNA-seq analysis, and recently I started working with ASAP Human Postmortem-Derived Brain Sequencing Collection data. I wanted to ask two questions regarding this dataset: Is there a protocol availab… --- ## [SEA-AD Multiome problems](https://community.brain-map.org/t/sea-ad-multiome-problems/4550)
**Author:** [@Victhagas](https://community.brain-map.org/u/Victhagas)\ **Replies:** 3\ **Last updated:** [July 24, 2025, 5:14pm UTC](https://community.brain-map.org/t/sea-ad-multiome-problems/4550 "2025-07-24T17:14:46Z")
Hi Guys! I was checking the Seattle Alzheimer’s Disease Brain Cell Atlas GitHub page and down at the data location part, I found this: “Briefly, the processed single nucleus RNAseq, ATACseq, and Multiome as well as MERF… --- ## [Using ABC atlas for publications](https://community.brain-map.org/t/using-abc-atlas-for-publications/4530)
**Author:** [@Pablo\_ValderramaC](https://community.brain-map.org/u/Pablo_ValderramaC)\ **Replies:** 4\ **Last updated:** [July 16, 2025, 8:33pm UTC](https://community.brain-map.org/t/using-abc-atlas-for-publications/4530 "2025-07-16T20:33:10Z")
Hello, I am working with a scRNAseq dataset of the hypothalamus, which I annotated with MapMyCells. Based on this, when I subcluster the tanycytes population I get one subcluster with all cells being part of the 1173\_tan… --- ## [New Parkinson's Disease Data Now Explorable in ABC Atlas](https://community.brain-map.org/t/new-parkinsons-disease-data-now-explorable-in-abc-atlas/4428)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [May 22, 2025, 2:12pm UTC](https://community.brain-map.org/t/new-parkinsons-disease-data-now-explorable-in-abc-atlas/4428 "2025-05-22T14:12:03Z")
The ABC Atlas has been updated with new data! We are proud to share new data produced by Aligning Science Across Parkinson’s (ASAP) researchers. The ASAP initiative, Allen Institute, and Michael J. Fox Foundation are t… --- ## [ABC Atlas Updates: Marker Genes](https://community.brain-map.org/t/abc-atlas-updates-marker-genes/4515)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 1\ **Last updated:** [July 11, 2025, 1:19pm UTC](https://community.brain-map.org/t/abc-atlas-updates-marker-genes/4515 "2025-07-11T13:19:10Z")
With this release, marker gene annotations for the Whole Mouse Brain taxonomy (Yao et al.) and the Whole Human Brain taxonomy (Siletti et al.) are available in ABC Atlas Cell Type Cards. Cell Type Cards now display the … --- ## [Retrograde Connectivity Data Release announcement](https://community.brain-map.org/t/retrograde-connectivity-data-release-announcement/4519)
**Author:** [@ray.sanchez](https://community.brain-map.org/u/ray.sanchez)\ **Replies:** 0\ **Last updated:** [July 9, 2025, 8:29pm UTC](https://community.brain-map.org/t/retrograde-connectivity-data-release-announcement/4519 "2025-07-09T20:29:35Z")
The Allen Institute for Brain Science is thrilled to announce the release of Retrograde Connectivity data through the Data Catalog. The Retrograde Connectivity data release provides Neuroglancer-based views of 249 Tissue… --- ## [Retrograde Connectivity Data Release: Reference documentation](https://community.brain-map.org/t/retrograde-connectivity-data-release-reference-documentation/4518)
**Author:** [@ray.sanchez](https://community.brain-map.org/u/ray.sanchez)\ **Replies:** 0\ **Last updated:** [July 9, 2025, 8:29pm UTC](https://community.brain-map.org/t/retrograde-connectivity-data-release-reference-documentation/4518 "2025-07-09T20:29:18Z")
Project Page You can access the Retrograde Connectivity data via the Data Catalog project page here. The Project page summarizes project metadata and links to funding information, protocols and data resources. The HIGH… --- ## [Tutorial: Finding AAVs for targeting Cholinergic cell populations in the striatum](https://community.brain-map.org/t/tutorial-finding-aavs-for-targeting-cholinergic-cell-populations-in-the-striatum/3673)
**Author:** [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Replies:** 0\ **Last updated:** [September 16, 2024, 4:12pm UTC](https://community.brain-map.org/t/tutorial-finding-aavs-for-targeting-cholinergic-cell-populations-in-the-striatum/3673 "2024-09-16T16:12:05Z")
As a scientist doing research on the Basal Ganglia, I’m looking for viral genetic tools that allow me to specifically target cell types in the striatum for an upcoming set of experiments. I use the Genetic Tools Atlas f… --- ## [Genetic Tools Atlas - Frequently Asked Questions (FAQs)](https://community.brain-map.org/t/genetic-tools-atlas-frequently-asked-questions-faqs/4175)
**Author:** [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Replies:** 0\ **Last updated:** [February 20, 2025, 4:47pm UTC](https://community.brain-map.org/t/genetic-tools-atlas-frequently-asked-questions-faqs/4175 "2025-02-20T16:47:23Z")
These frequently asked questions (FAQs) center around the Genetic Tools Atlas, a searchable web tool representing information and data on enhancer-adeno-associated viruses (enhancer AAVs) and mouse transgenes characteriz… --- ## [Using Neuroglancer to Explore Images](https://community.brain-map.org/t/using-neuroglancer-to-explore-images/4514)
**Author:** [@ray.sanchez](https://community.brain-map.org/u/ray.sanchez)\ **Replies:** 0\ **Last updated:** [July 8, 2025, 4:36pm UTC](https://community.brain-map.org/t/using-neuroglancer-to-explore-images/4514 "2025-07-08T16:36:13Z")
Neuroglancer Neuroglancer is web-based image viewer for volumetric data. Neuroglancer renders data from OME-Zarr files, which are optimized for storing large, n-dimensional arrays in the cloud. You can use Neuroglancer t… --- ## [Selecting more than 100 cells](https://community.brain-map.org/t/selecting-more-than-100-cells/4503)
**Author:** [@RSBDZ](https://community.brain-map.org/u/RSBDZ)\ **Replies:** 4\ **Last updated:** [July 4, 2025, 1:16am UTC](https://community.brain-map.org/t/selecting-more-than-100-cells/4503 "2025-07-04T01:16:31Z")
Hello Regarding your statement: “While in the Cell Selection view, details of the selected cells can be downloaded as a csv file. Please note, only the first 100 cells will be included in the download. Full dataset down… --- ## [How to access pre-calculated ephys data for comparison of ephy properties of different MET types?](https://community.brain-map.org/t/how-to-access-pre-calculated-ephys-data-for-comparison-of-ephy-properties-of-different-met-types/4497)
**Author:** [@pcmaaaaa](https://community.brain-map.org/u/pcmaaaaa)\ **Replies:** 1\ **Last updated:** [June 30, 2025, 8:34pm UTC](https://community.brain-map.org/t/how-to-access-pre-calculated-ephys-data-for-comparison-of-ephy-properties-of-different-met-types/4497 "2025-06-30T20:34:17Z")
I’m trying to compare the ephys properties such as resting potentials of different types of interneurons. The Brain Knowledge Platform provides visualization of the pre-calculated ephys properties of each specimen of dif… --- ## [Inquiry About Human Gene Markers in MapMyCells](https://community.brain-map.org/t/inquiry-about-human-gene-markers-in-mapmycells/4402)
**Author:** [@Javier](https://community.brain-map.org/u/Javier)\ **Replies:** 3\ **Last updated:** [June 30, 2025, 3:13pm UTC](https://community.brain-map.org/t/inquiry-about-human-gene-markers-in-mapmycells/4402 "2025-06-30T15:13:58Z")
Hello, Thank you for the fantastic tool! I’ve been searching for the list of gene markers used for annotating human region-specific subtypes in MapMyCells. I was able to find the mouse annotation table here: Whole adul… --- ## [Mapping to Brain region](https://community.brain-map.org/t/mapping-to-brain-region/3182)
**Author:** [@koenvandenberge](https://community.brain-map.org/u/koenvandenberge)\ **Replies:** 5\ **Last updated:** [June 13, 2025, 8:25am UTC](https://community.brain-map.org/t/mapping-to-brain-region/3182 "2025-06-13T08:25:15Z")
Hi, I was successfully able to use MapMyCells, which is a tremendous tool for the community. The output shows cell class and subclass labels for each mapped cell. However, I am more interested in predicting regions whe… --- ## [Low diversity in mapped results](https://community.brain-map.org/t/low-diversity-in-mapped-results/4398)
**Author:** [@cmccormick](https://community.brain-map.org/u/cmccormick)\ **Replies:** 15\ **Last updated:** [May 28, 2025, 3:51pm UTC](https://community.brain-map.org/t/low-diversity-in-mapped-results/4398 "2025-05-28T15:51:02Z")
When using MapMyCells with a snRNAseq dataset produced from mouse brain samples I was able to successfully map my data. However, when looking at the results, a vast majority (though not all) of the cells are being mapped… --- ## [Documentation: Mouse Spinal Cord](https://community.brain-map.org/t/documentation-mouse-spinal-cord/3769)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [October 17, 2024, 3:58pm UTC](https://community.brain-map.org/t/documentation-mouse-spinal-cord/3769 "2024-10-17T15:58:32Z")
Document Description Overview Technical white paper describing the methodology for the project. Reference Atlas Technical white paper describing the methodology for the reference atlas. Expression Categories T… --- ## [Difference between data from the AllenSDK and the webpage](https://community.brain-map.org/t/difference-between-data-from-the-allensdk-and-the-webpage/3834)
**Author:** [@DavideR](https://community.brain-map.org/u/DavideR)\ **Replies:** 1\ **Last updated:** [May 19, 2025, 11:49am UTC](https://community.brain-map.org/t/difference-between-data-from-the-allensdk-and-the-webpage/3834 "2025-05-19T11:49:15Z")
I was downloading some connectivity data through the AllenSKD package. I want to have connection data from all the brain structures, projecting to a specific target, so i did: # import libraries and API from allensdk.co… --- ## [ABC Atlas Updates: Introducing Cell Type Cards](https://community.brain-map.org/t/abc-atlas-updates-introducing-cell-type-cards/4400)
**Author:** [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\ **Replies:** 0\ **Last updated:** [May 12, 2025, 11:50pm UTC](https://community.brain-map.org/t/abc-atlas-updates-introducing-cell-type-cards/4400 "2025-05-12T23:50:38Z")
With this release we introduce an exciting new feature to the ABC Atlas: Cell Type Cards! When viewing a cell type in ABC Atlas, additional information about the taxon is now just a click away. There are two ways to ope… --- ## [Human Brain Atlas: In Situ Hybridization (ISH) Data](https://community.brain-map.org/t/human-brain-atlas-in-situ-hybridization-ish-data/2872)
**Author:** [@ray.sanchez](https://community.brain-map.org/u/ray.sanchez)\ **Replies:** 4\ **Last updated:** [May 1, 2025, 9:01pm UTC](https://community.brain-map.org/t/human-brain-atlas-in-situ-hybridization-ish-data/2872 "2025-05-01T21:01:26Z")
Searching Gene Search Search by Study Gene Classification Viewing Images Experiment Details Page Zoom and Pan (ZAP) Image Viewer High Resolution Image Viewer Specimen Detail Information Gene expression data is av… --- ## [Human Cortical Layer Markers](https://community.brain-map.org/t/human-cortical-layer-markers/4355)
**Author:** [@MPanday](https://community.brain-map.org/u/MPanday)\ **Replies:** 2\ **Last updated:** [May 1, 2025, 8:56pm UTC](https://community.brain-map.org/t/human-cortical-layer-markers/4355 "2025-05-01T20:56:30Z")
Hi There, A quick question. I know that the database can be filtered for a series of different disease or development gene families, but is there a list of cortical layer marker genes in documentation that I can access?… --- ## [Error in build\_orthology\_table](https://community.brain-map.org/t/error-in-build-orthology-table/4318)
**Author:** [@lizchcase](https://community.brain-map.org/u/lizchcase)\ **Replies:** 4\ **Last updated:** [April 15, 2025, 5:53pm UTC](https://community.brain-map.org/t/error-in-build-orthology-table/4318 "2025-04-15T17:53:55Z")
I’m looking to use MapMyCells on a naked mole-rat dataset, so I’m going through the process of finding orthologous genes found on the GeneOrthology github page. I really only need orthologs between mice and NMRs, so I ra… --- ## [How to get the raster plot about V1 GLIF point neuron model](https://community.brain-map.org/t/how-to-get-the-raster-plot-about-v1-glif-point-neuron-model/4308)
**Author:** [@chenyiyi](https://community.brain-map.org/u/chenyiyi)\ **Replies:** 2\ **Last updated:** [April 11, 2025, 8:50pm UTC](https://community.brain-map.org/t/how-to-get-the-raster-plot-about-v1-glif-point-neuron-model/4308 "2025-04-11T20:50:04Z")
Hello! I am studying the paper “Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex”, and I am doing some reproduction work according to the guidance of the p… --- ## [Has MMC changed? Completely different results on identical datasets](https://community.brain-map.org/t/has-mmc-changed-completely-different-results-on-identical-datasets/4270)
**Author:** [@MathieuBourdenx](https://community.brain-map.org/u/MathieuBourdenx)\ **Replies:** 6\ **Last updated:** [April 3, 2025, 4:39pm UTC](https://community.brain-map.org/t/has-mmc-changed-completely-different-results-on-identical-datasets/4270 "2025-04-03T16:39:06Z")
Good morning, I was obtaining odd results with new datasets from mouse brain until I decided to resubmit an h5ad file that I had submitted 2 months ago. I am showing here the distribution of bootstrapping probability at… --- ## [Error in data output in MapMyCells](https://community.brain-map.org/t/error-in-data-output-in-mapmycells/4237)
**Author:** [@mrazzoli](https://community.brain-map.org/u/mrazzoli)\ **Replies:** 17\ **Last updated:** [April 3, 2025, 2:53pm UTC](https://community.brain-map.org/t/error-in-data-output-in-mapmycells/4237 "2025-04-03T14:53:32Z")
I’m adapting a spatial transcriptomics dataset to load into MapMyCells. It’s mouse data and I’m working the R Studio environment. I downloaded the R script but I hit a roadblock when attempting the first step for generat… [Previous page](https://community.brain-map.org/c/how-to/15.md?page=1) [Next page](https://community.brain-map.org/c/how-to/15.md?page=3)