# \#atlas-mouse-brain-adult **URL:** https://community.brain-map.org/tag/atlas-mouse-brain-adult/8.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) --- ## [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… --- ## [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? --- ## [Unit of the Merfish coordinates](https://community.brain-map.org/t/unit-of-the-merfish-coordinates/4889)
**Author:** [@wykpenguin](https://community.brain-map.org/u/wykpenguin)\ **Replies:** 1\ **Last updated:** [June 5, 2026, 1:16pm UTC](https://community.brain-map.org/t/unit-of-the-merfish-coordinates/4889 "2026-06-05T13:16:43Z")
I want to use the Allen Merfish data for spatial analysis, what are the units of the x\_reconstructed and y\_reconstructed data? A typical section is around 6x6 units in x and y, seems too small to be mm or micron. I need … --- ## [Normalizing imputed spatial dataset](https://community.brain-map.org/t/normalizing-imputed-spatial-dataset/4886)
**Author:** [@wykpenguin](https://community.brain-map.org/u/wykpenguin)\ **Replies:** 1\ **Last updated:** [April 22, 2026, 3:29pm UTC](https://community.brain-map.org/t/normalizing-imputed-spatial-dataset/4886 "2026-04-22T15:29:19Z")
The inputed spatial transcriptomics data is only available in log2 transformed form. Some downstream analysis requires normalized data. What is the best way of doing this? Can I get back to the raw counts by 2^(log2 valu… --- ## [Missing R2 FASTQ files for Patch-seq dataset](https://community.brain-map.org/t/missing-r2-fastq-files-for-patch-seq-dataset/4852)
**Author:** [@nuo\_xu](https://community.brain-map.org/u/nuo_xu)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 3:01am UTC](https://community.brain-map.org/t/missing-r2-fastq-files-for-patch-seq-dataset/4852 "2026-04-08T03:01:07Z")
Hello, The methods section in the paper “Connecting single-cell transcriptomes to projectomes in mouse visual cortex" states that libraries were sequenced as “fifty-base-pair paired-end reads.” However, when downloading… --- ## [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! --- ## [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… --- ## [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… --- ## [Assistance needed in using Allen 3D atlas to merge with PET CT](https://community.brain-map.org/t/assistance-needed-in-using-allen-3d-atlas-to-merge-with-pet-ct/4765)
**Author:** [@Dr-Parsi2025](https://community.brain-map.org/u/Dr-Parsi2025)\ **Replies:** 2\ **Last updated:** [December 17, 2025, 10:16pm UTC](https://community.brain-map.org/t/assistance-needed-in-using-allen-3d-atlas-to-merge-with-pet-ct/4765 "2025-12-17T22:16:23Z")
Good day! I have downloaded average\_template\_50.nii and want to merge it with PET CT file in 3D slicer or any similar software related to Radiology and neuroscience. The issue I am facing is that it seems the size of at… --- ## [Trouble aligning flattened brains to CCFv3 ](https://community.brain-map.org/t/trouble-aligning-flattened-brains-to-ccfv3/4775)
**Author:** [@JemmaY31](https://community.brain-map.org/u/JemmaY31)\ **Replies:** 1\ **Last updated:** [December 4, 2025, 6:41pm UTC](https://community.brain-map.org/t/trouble-aligning-flattened-brains-to-ccfv3/4775 "2025-12-04T18:41:22Z")
Hi everyone, I’m currently using the ABBA pipeline to align whole-brain images to the Allen Brain Atlas (CCFv3). However, because my mice had a metal head-fixed pedestal for behavioral experiments, the brain appears to … --- ## [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! --- ## [ISH false discovery rate (fdr)](https://community.brain-map.org/t/ish-false-discovery-rate-fdr/4728)
**Author:** [@AKAnderson](https://community.brain-map.org/u/AKAnderson)\ **Replies:** 0\ **Last updated:** [October 24, 2025, 6:26pm UTC](https://community.brain-map.org/t/ish-false-discovery-rate-fdr/4728 "2025-10-24T18:26:33Z")
In the ISH dataset of mice, there is a fold change data for each gene, but there is not false discovery rate data (fdr). Is there a way to get this information? I am trying to generate a volcano plot. Thanks for any insi… --- ## [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 --- ## [MERFISH sample id on BIL](https://community.brain-map.org/t/merfish-sample-id-on-bil/4639)
**Author:** [@simonf](https://community.brain-map.org/u/simonf)\ **Replies:** 2\ **Last updated:** [August 13, 2025, 11:13am UTC](https://community.brain-map.org/t/merfish-sample-id-on-bil/4639 "2025-08-13T11:13:04Z")
Hi, I was looking for MERFISH mouse brain raw data on BIL, however was struggling to assign the correct samples. Any documentation/clarification would be appreciated! ABC Atlas (Yao 2023 Nature) links to https://doi.b… --- ## [Estimate location of brain sagittal or coronal slice](https://community.brain-map.org/t/estimate-location-of-brain-sagittal-or-coronal-slice/4473)
**Author:** [@koenvandenberge](https://community.brain-map.org/u/koenvandenberge)\ **Replies:** 1\ **Last updated:** [August 12, 2025, 7:05pm UTC](https://community.brain-map.org/t/estimate-location-of-brain-sagittal-or-coronal-slice/4473 "2025-08-12T19:05:11Z")
Hi All, We are working with a spatial transcriptomics dataset (Xenium and/or CosMx) where we have several samples, say using a coronal brain slice. Some slices were taken at slightly different locations/angles than othe… --- ## [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… --- ## [Extracting data for all genes from an ROI](https://community.brain-map.org/t/extracting-data-for-all-genes-from-an-roi/507)
**Author:** [@vbhave](https://community.brain-map.org/u/vbhave)\ **Replies:** 10\ **Last updated:** [August 4, 2025, 6:52pm UTC](https://community.brain-map.org/t/extracting-data-for-all-genes-from-an-roi/507 "2025-08-04T18:52:09Z")
I was writing to ask about how we might obtain a full gene expression dataset for a handful of brain regions from the adult mouse (e.g. the DR and PAG). We’re interested in getting data by anatomical region as opposed t… --- ## [Getting structure masks for fine substructures](https://community.brain-map.org/t/getting-structure-masks-for-fine-substructures/4509)
**Author:** [@terrenceM](https://community.brain-map.org/u/terrenceM)\ **Replies:** 4\ **Last updated:** [July 6, 2025, 6:27pm UTC](https://community.brain-map.org/t/getting-structure-masks-for-fine-substructures/4509 "2025-07-06T18:27:37Z")
Hi there, The Allen atlas has fine substructures for some regions (e.g. subregions of SCig, here). I can find the structure ids associated with them, for example with the below code scm\_sub\_acronyms = \['SCig-a', 'SCd… --- ## [Having trouble finding MET data all for the same cell from specific paper](https://community.brain-map.org/t/having-trouble-finding-met-data-all-for-the-same-cell-from-specific-paper/4405)
**Author:** [@dom\_pols](https://community.brain-map.org/u/dom_pols)\ **Replies:** 3\ **Last updated:** [June 20, 2025, 8:56pm UTC](https://community.brain-map.org/t/having-trouble-finding-met-data-all-for-the-same-cell-from-specific-paper/4405 "2025-06-20T20:56:39Z")
Thus far, I have been looking at all the data found on this page: Multimodal Characterization in Mouse Visual Cortex - brain-map.org for the combined morphology, electrophysiology, and transcriptome data for individual … --- ## [Error when attempting differential search in Mouse Brain Atlas](https://community.brain-map.org/t/error-when-attempting-differential-search-in-mouse-brain-atlas/4456)
**Author:** [@Zahraa](https://community.brain-map.org/u/Zahraa)\ **Replies:** 6\ **Last updated:** [June 6, 2025, 12:25pm UTC](https://community.brain-map.org/t/error-when-attempting-differential-search-in-mouse-brain-atlas/4456 "2025-06-06T12:25:59Z")
Hi. I’m trying to conduct a differential search with the target being the Primary Visual Area Layer 2/3 and the contrast structure being the Isocortex (by clicking on the suggested search prompt), but I keep coming up a… --- ## [Mouse reference atlas areas volume](https://community.brain-map.org/t/mouse-reference-atlas-areas-volume/3072)
**Author:** [@aldupin](https://community.brain-map.org/u/aldupin)\ **Replies:** 2\ **Last updated:** [June 5, 2025, 3:35pm UTC](https://community.brain-map.org/t/mouse-reference-atlas-areas-volume/3072 "2025-06-05T15:35:19Z")
Hello, I am wondering how to access the data of brain areas volumes (or number of cell) for the adult mouse reference atlas ? I would need it to normalize some quantifications I am doing. Thanks in advance ! --- ## [Differentiating ISH signals from background](https://community.brain-map.org/t/differentiating-ish-signals-from-background/2309)
**Author:** [@trmurphy39](https://community.brain-map.org/u/trmurphy39)\ **Replies:** 2\ **Last updated:** [April 21, 2025, 6:59am UTC](https://community.brain-map.org/t/differentiating-ish-signals-from-background/2309 "2025-04-21T06:59:46Z")
Hello, I have a rather elementary question on how to interpret the Allen Brain mouse ISH data. Since there was no counterstain used in these experiments, any visible chromogenic signals should presumably represent targe… --- ## [Bregma standard?](https://community.brain-map.org/t/bregma-standard/4282)
**Author:** [@Paulahyns](https://community.brain-map.org/u/Paulahyns)\ **Replies:** 1\ **Last updated:** [April 3, 2025, 6:07am UTC](https://community.brain-map.org/t/bregma-standard/4282 "2025-04-03T06:07:24Z")
Hello, I am trying to determine how to best replicate the stereotactic coordinates used in the connectivity atlas. It seems there are a number of different ways that Bregma can be defined and many publications do not re… --- ## [Retrieving the volume of mouse brain structures with allensdk](https://community.brain-map.org/t/retrieving-the-volume-of-mouse-brain-structures-with-allensdk/4050)
**Author:** [@JuCorbo](https://community.brain-map.org/u/JuCorbo)\ **Replies:** 3\ **Last updated:** [April 2, 2025, 3:02pm UTC](https://community.brain-map.org/t/retrieving-the-volume-of-mouse-brain-structures-with-allensdk/4050 "2025-04-02T15:02:44Z")
Hi I have a dataset of cell counts that was generated using the mouse brain atlas’ segmentation. I want to normalize the counts using the structures’ volume in the atlas. I am trying to use the sdk in python to retrieve… --- ## [Why The Edge of MEC and LEC different between Allen Atlas and Paxinos Stereotaxic Coordinates?](https://community.brain-map.org/t/why-the-edge-of-mec-and-lec-different-between-allen-atlas-and-paxinos-stereotaxic-coordinates/4136)
**Author:** [@Rick\_Yuuu](https://community.brain-map.org/u/Rick_Yuuu)\ **Replies:** 2\ **Last updated:** [February 18, 2025, 10:27am UTC](https://community.brain-map.org/t/why-the-edge-of-mec-and-lec-different-between-allen-atlas-and-paxinos-stereotaxic-coordinates/4136 "2025-02-18T10:27:24Z")
The sagittal atlas at about lateral 3.36 mm of Allen map and Paxinos is: The Dorsal part of MEC in Paxinos was attributed to LEC in Allen map. This really troubles my resarch, for we’re preparing for MEC imaging. W… --- ## [New abc\_atlas\_acces release with Aging Mouse Data](https://community.brain-map.org/t/new-abc-atlas-acces-release-with-aging-mouse-data/4003)
**Author:** [@morriscb](https://community.brain-map.org/u/morriscb)\ **Replies:** 0\ **Last updated:** [December 18, 2024, 11:28pm UTC](https://community.brain-map.org/t/new-abc-atlas-acces-release-with-aging-mouse-data/4003 "2024-12-18T23:28:10Z")
Hi everyone, We’re happy to announce the release of the Aging Mouse dataset via the abc\_atlas\_access tool. A full release through the ABC Atlas visualization will be coming in the future. This data release includes des… --- ## [How to get a specimen stack space(volume) from an mouse ISH section dataset or get an actual coodinates of point alignment in reference space?](https://community.brain-map.org/t/how-to-get-a-specimen-stack-space-volume-from-an-mouse-ish-section-dataset-or-get-an-actual-coodinates-of-point-alignment-in-reference-space/3822)
**Author:** [@tanzhengtang](https://community.brain-map.org/u/tanzhengtang)\ **Replies:** 1\ **Last updated:** [November 1, 2024, 9:53am UTC](https://community.brain-map.org/t/how-to-get-a-specimen-stack-space-volume-from-an-mouse-ish-section-dataset-or-get-an-actual-coodinates-of-point-alignment-in-reference-space/3822 "2024-11-01T09:53:51Z")
Dear Allen Brain Atlas Team, In this page, API for Mouse Brain Atlas, the author write this Once registration is achieved, information from the 3-D reference model can be transferred to the reconstructed Specimen and vi… --- ## [How to use "Mouse Whole Cortex and Hippocampus 10x" to annotate a spatial data set in seuart?](https://community.brain-map.org/t/how-to-use-mouse-whole-cortex-and-hippocampus-10x-to-annotate-a-spatial-data-set-in-seuart/2333)
**Author:** [@ivingan01](https://community.brain-map.org/u/ivingan01)\ **Replies:** 2\ **Last updated:** [June 1, 2023, 7:35pm UTC](https://community.brain-map.org/t/how-to-use-mouse-whole-cortex-and-hippocampus-10x-to-annotate-a-spatial-data-set-in-seuart/2333 "2023-06-01T19:35:40Z")
Hi Allen Brian Map Community, Long time listener, first time caller. I am a novice to coding and data analysis. I am working my way through the seurat tutorial to analyze spatial transcriptomic data (Analysis, visualiz… --- ## [Regional cell taxonomy](https://community.brain-map.org/t/regional-cell-taxonomy/3746)
**Author:** [@scanchi](https://community.brain-map.org/u/scanchi)\ **Replies:** 3\ **Last updated:** [October 15, 2024, 5:51pm UTC](https://community.brain-map.org/t/regional-cell-taxonomy/3746 "2024-10-15T17:51:05Z")
Hello All, Thank you for providing the community with both the resources and tools for taxonomy assignment. Our lab is interested in developing region specific reference for our analysis purposes. I have been using the … --- ## [Mask a mouse brain slice image by ROI or ROI's from a projection experiment](https://community.brain-map.org/t/mask-a-mouse-brain-slice-image-by-roi-or-rois-from-a-projection-experiment/3678)
**Author:** [@jonahb](https://community.brain-map.org/u/jonahb)\ **Replies:** 2\ **Last updated:** [October 8, 2024, 6:30pm UTC](https://community.brain-map.org/t/mask-a-mouse-brain-slice-image-by-roi-or-rois-from-a-projection-experiment/3678 "2024-10-08T18:30:25Z")
Can I mask a brain slice image, programatically or some other way, so that it only shows a given region of interest (eg. a layer of cortex) and the florescence data in it? [Next page](https://community.brain-map.org/tag/atlas-mouse-brain-adult/8.md?match_all_tags=true&page=1&tags%5B%5D=atlas-mouse-brain-adult)