# \#how-to **URL:** https://community.brain-map.org/tag/how-to/46.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) --- ## [Brian explorer 2](https://community.brain-map.org/t/brian-explorer-2/4855)
**Author:** [@anna.nigri](https://community.brain-map.org/u/anna.nigri)\ **Replies:** 10\ **Last updated:** [October 16, 2026, 9:56pm UTC](https://community.brain-map.org/t/brian-explorer-2/4855 "2026-10-16T21:56:59Z")
Dear, I recently downloaded and installed Brain Explorer 2 for Windows, but when I launch the program I receive the following error message: “Could not retrieve atlas list from http://www.brain-map.org. No atlas avail… --- ## [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:** 3\ **Last updated:** [September 29, 2026, 9:32am UTC](https://community.brain-map.org/t/how-to-start-do-wgcna-of-microarray-datasets/5073 "2026-09-29T09:32:26Z")
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… --- ## [Replicating Fig 3c — request for lmplots source from helper\_functions.py](https://community.brain-map.org/t/replicating-fig-3c-request-for-lmplots-source-from-helper-functions-py/4963)
**Author:** [@granzota](https://community.brain-map.org/u/granzota)\ **Replies:** 2\ **Last updated:** [June 23, 2026, 10:07am UTC](https://community.brain-map.org/t/replicating-fig-3c-request-for-lmplots-source-from-helper-functions-py/4963 "2026-06-23T10:07:47Z")
Dear all, I am writing for clarification on the implementation of the lmplots function used to generate Figure 3c of Gabitto et al. 2024 (Nature Neuroscience). In the context of a project on a subpopulation in MTG, I h… --- ## [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 … --- ## [Human Brain Atlas Mesh Files](https://community.brain-map.org/t/human-brain-atlas-mesh-files/560)
**Author:** [@jopeter](https://community.brain-map.org/u/jopeter)\ **Replies:** 6\ **Last updated:** [June 2, 2026, 4:42am UTC](https://community.brain-map.org/t/human-brain-atlas-mesh-files/560 "2026-06-02T04:42:52Z")
Hello, I was wondering if the Allen Institute provides structural meshes for a segmented human reference brain similar to the mouse ccf meshes provided here: http://download.alleninstitute.org/informatics-archive/curren… --- ## [Freezing of isolated nuclei](https://community.brain-map.org/t/freezing-of-isolated-nuclei/1081)
**Author:** [@Martina17](https://community.brain-map.org/u/Martina17)\ **Replies:** 2\ **Last updated:** [May 11, 2026, 1:54pm UTC](https://community.brain-map.org/t/freezing-of-isolated-nuclei/1081 "2026-05-11T13:54:26Z")
Hi, I am isolating nuclei from snap frozen brain tissue (prefrontal cortex). The nuclei are then used to perform single-nuclei RNA seq using 10x genomics technology. I normally extract the nuclei from the tissue and th… --- ## [How to download a small of subset of single-cell multiomics (RNA/ATAC) of a small brain region?](https://community.brain-map.org/t/how-to-download-a-small-of-subset-of-single-cell-multiomics-rna-atac-of-a-small-brain-region/4768)
**Author:** [@Chris\_D](https://community.brain-map.org/u/Chris_D)\ **Replies:** 5\ **Last updated:** [April 14, 2026, 1:24pm UTC](https://community.brain-map.org/t/how-to-download-a-small-of-subset-of-single-cell-multiomics-rna-atac-of-a-small-brain-region/4768 "2026-04-14T13:24:43Z")
Hi all, I am trying to download a small subset of single-cell multiomics but have difficult to find out how after reading related paper and navigate this website. Would you please have a guidance? I went to https://know… --- ## [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… --- ## [Access to raw recordings of 2-photon calcium imaging for studying visual behaviour in mice](https://community.brain-map.org/t/access-to-raw-recordings-of-2-photon-calcium-imaging-for-studying-visual-behaviour-in-mice/4795)
**Author:** [@Ermes](https://community.brain-map.org/u/Ermes)\ **Replies:** 1\ **Last updated:** [January 12, 2026, 11:56pm UTC](https://community.brain-map.org/t/access-to-raw-recordings-of-2-photon-calcium-imaging-for-studying-visual-behaviour-in-mice/4795 "2026-01-12T23:56:32Z")
Hi all, I am interested in performing some analyses on the visual behaviour 2P Ca2+ imaging dataset and am currently trying to reconstruct raw movies of recorded Ca2+ activity by combining the df/f signal with average p… --- ## [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… --- ## [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… --- ## [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? --- ## [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 … --- ## [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… --- ## [Mouse brain reference atlases & mapping your own data](https://community.brain-map.org/t/mouse-brain-reference-atlases-mapping-your-own-data/243)
**Author:** [@brain](https://community.brain-map.org/u/brain)\ **Replies:** 8\ **Last updated:** [September 25, 2025, 2:11am UTC](https://community.brain-map.org/t/mouse-brain-reference-atlases-mapping-your-own-data/243 "2025-09-25T02:11:55Z")
How do I map my data to your reference atlas? We have been hearing this question (or variants of it) for as long as the Allen Mouse Brain Atlas has been online. The short answer is, We do not have a tool for this - b… --- ## [Generating Expression Masks De Novo](https://community.brain-map.org/t/generating-expression-masks-de-novo/4440)
**Author:** [@MPanday](https://community.brain-map.org/u/MPanday)\ **Replies:** 1\ **Last updated:** [August 21, 2025, 1:19pm UTC](https://community.brain-map.org/t/generating-expression-masks-de-novo/4440 "2025-08-21T13:19:57Z")
Hello @tylermo @wayne I’ve been using expression images for large-scale, high-content analysis of cell morphology in the mouse ISH database. I would like to know if there’s a way for me to process my own image data to p… --- ## [Downloading gene expression data for the different mouse brain regions (expressed/not expressed) as a list](https://community.brain-map.org/t/downloading-gene-expression-data-for-the-different-mouse-brain-regions-expressed-not-expressed-as-a-list/4641)
**Author:** [@Zsofi6](https://community.brain-map.org/u/Zsofi6)\ **Replies:** 2\ **Last updated:** [August 18, 2025, 2:23pm UTC](https://community.brain-map.org/t/downloading-gene-expression-data-for-the-different-mouse-brain-regions-expressed-not-expressed-as-a-list/4641 "2025-08-18T14:23:00Z")
Hi there, I am looking to understand the expression of individual genes across the different mouse brain regions. I am really looking for a list of areas where my gene of interest is expressed, that can be downloaded in… --- ## [Registering partial 2D IHC images to Allen Brain Atlas using QuickNII](https://community.brain-map.org/t/registering-partial-2d-ihc-images-to-allen-brain-atlas-using-quicknii/4651)
**Author:** [@michelletytong](https://community.brain-map.org/u/michelletytong)\ **Replies:** 2\ **Last updated:** [August 16, 2025, 7:04pm UTC](https://community.brain-map.org/t/registering-partial-2d-ihc-images-to-allen-brain-atlas-using-quicknii/4651 "2025-08-16T19:04:27Z")
Hi all, I’m wondering if anyone else has successfully used QuickNII to register IHC images of specific brain regions to the Allen Brain Atlas. We have an IHC dataset of just the hippocampal formation, with 3-4 channels … --- ## [Trouble Download xml file from ISH Differential search results](https://community.brain-map.org/t/trouble-download-xml-file-from-ish-differential-search-results/4646)
**Author:** [@AKAnderson](https://community.brain-map.org/u/AKAnderson)\ **Replies:** 4\ **Last updated:** [August 15, 2025, 5:55pm UTC](https://community.brain-map.org/t/trouble-download-xml-file-from-ish-differential-search-results/4646 "2025-08-15T17:55:51Z")
Hello, I’m having trouble downloading the xml file and converting/importing it into an excel. When I selected the xml link at the bottom of my results page, download it, and load it into excel, there is no data within t… --- ## [Differential search (Human Brain)](https://community.brain-map.org/t/differential-search-human-brain/950)
**Author:** [@paolo](https://community.brain-map.org/u/paolo)\ **Replies:** 4\ **Last updated:** [August 13, 2025, 8:34pm UTC](https://community.brain-map.org/t/differential-search-human-brain/950 "2025-08-13T20:34:02Z")
Is it possible to filter the results of a differential search by a gene? Or alternatively, is there a way to download all the results in a single file? --- ## [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 … --- ## [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… --- ## [Batch download: Developing mouse brain](https://community.brain-map.org/t/batch-download-developing-mouse-brain/4602)
**Author:** [@ddofer](https://community.brain-map.org/u/ddofer)\ **Replies:** 8\ **Last updated:** [August 11, 2025, 3:25pm UTC](https://community.brain-map.org/t/batch-download-developing-mouse-brain/4602 "2025-08-11T15:25:32Z")
I want to download the data for all available genes in the developing mouse brain dataset, across all time-points, mapped to the highest level/coarsest Structure Unionization level (i.e neuroanatomical region). The exam… --- ## [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… --- ## [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,… --- ## [Anyone familiar with studies on consciousness in computational neuroscience?](https://community.brain-map.org/t/anyone-familiar-with-studies-on-consciousness-in-computational-neuroscience/4420)
**Author:** [@GitItD](https://community.brain-map.org/u/GitItD)\ **Replies:** 1\ **Last updated:** [May 27, 2025, 8:57pm UTC](https://community.brain-map.org/t/anyone-familiar-with-studies-on-consciousness-in-computational-neuroscience/4420 "2025-05-27T20:57:12Z")
Hello, I am a first year PhD student in computational biology, interested in diverging my research into computational neuroscience. Currently, I am interested in studies on consciousness in computational neuroscience/bio… --- ## [Accessing putative cell type in neuropixel dataset](https://community.brain-map.org/t/accessing-putative-cell-type-in-neuropixel-dataset/381)
**Author:** [@dwyrick](https://community.brain-map.org/u/dwyrick)\ **Replies:** 9\ **Last updated:** [April 24, 2025, 10:47pm UTC](https://community.brain-map.org/t/accessing-putative-cell-type-in-neuropixel-dataset/381 "2025-04-24T22:47:37Z")
Hello, I’m trying to utilize the neuropixel sessions that have inhibitory cell types identified via opto-tagging, but it doesn’t seem as if anything is written to take the responses during those optogenetic epochs and c… --- ## [Is there a cell type taxonomy of mouse in the hippocampus?](https://community.brain-map.org/t/is-there-a-cell-type-taxonomy-of-mouse-in-the-hippocampus/4268)
**Author:** [@YSivannn](https://community.brain-map.org/u/YSivannn)\ **Replies:** 4\ **Last updated:** [March 20, 2025, 3:54pm UTC](https://community.brain-map.org/t/is-there-a-cell-type-taxonomy-of-mouse-in-the-hippocampus/4268 "2025-03-20T15:54:07Z")
Hi there, I am analyzing gene expression across different cell types, such as excitatory and inhibitory neurons. However, I am quite confused because the taxonomy for excitatory and inhibitory neurons is only provided f… --- ## [Downloading full resolution images using AllenSDK](https://community.brain-map.org/t/downloading-full-resolution-images-using-allensdk/4123)
**Author:** [@mpj](https://community.brain-map.org/u/mpj)\ **Replies:** 5\ **Last updated:** [February 24, 2025, 6:19pm UTC](https://community.brain-map.org/t/downloading-full-resolution-images-using-allensdk/4123 "2025-02-24T18:19:01Z")
Hello All, This is my first post to the forum, so apologies if I am posting in the wrong category or with the wrong tags. I am trying to download full-scale nissl stain images of the human brain atlas (Experiment Detai… --- ## [Neocortex and SATB2 expression](https://community.brain-map.org/t/neocortex-and-satb2-expression/4139)
**Author:** [@Joanna](https://community.brain-map.org/u/Joanna)\ **Replies:** 1\ **Last updated:** [February 14, 2025, 8:04pm UTC](https://community.brain-map.org/t/neocortex-and-satb2-expression/4139 "2025-02-14T20:04:02Z")
Hello, I’m just beginning my exploration of the available data. I started with Brain Explorer, searching for neocortex and SATB2 expression, but I haven’t been able to find it. Could you provide any guidance on whether … [Next page](https://community.brain-map.org/tag/how-to/46.md?match_all_tags=true&page=1&tags%5B%5D=how-to)