# General **URL:** https://community.brain-map.org/c/general/1.md?page=4 [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:** 5 --- ## [Where to access coordinates for all unclassified cells?](https://community.brain-map.org/t/where-to-access-coordinates-for-all-unclassified-cells/3472)
**Author:** [@ycqiu](https://community.brain-map.org/u/ycqiu)\ **Replies:** 0\ **Last updated:** [July 11, 2024, 7:13am UTC](https://community.brain-map.org/t/where-to-access-coordinates-for-all-unclassified-cells/3472 "2024-07-11T07:13:32Z")
I am trying to download the data for both ZhuangABCA and MERFISH-C57BL6J-638850. But I couldn’t find complete sets of spatial coordinates for them. Spatial coordinates provided in metadata.csv only include cells that h… --- ## [How to download the original 1675 STPT images data of mouse brain that used for the Allen mouse atlas?](https://community.brain-map.org/t/how-to-download-the-original-1675-stpt-images-data-of-mouse-brain-that-used-for-the-allen-mouse-atlas/3462)
**Author:** [@tuyue](https://community.brain-map.org/u/tuyue)\ **Replies:** 0\ **Last updated:** [July 9, 2024, 7:45am UTC](https://community.brain-map.org/t/how-to-download-the-original-1675-stpt-images-data-of-mouse-brain-that-used-for-the-allen-mouse-atlas/3462 "2024-07-09T07:45:15Z")
Hi all, I have encountered some challenges while studying and utilizing the Allen Mouse Brain Atlas. As detailed in the paper titled “The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas,” the CCFv3 r… --- ## [Request for Permission to Publish Content by PLOS](https://community.brain-map.org/t/request-for-permission-to-publish-content-by-plos/3417)
**Author:** [@JianKLiu](https://community.brain-map.org/u/JianKLiu)\ **Replies:** 4\ **Last updated:** [June 26, 2024, 7:14am UTC](https://community.brain-map.org/t/request-for-permission-to-publish-content-by-plos/3417 "2024-06-26T07:14:36Z")
Hello, fellows, We are working on a manuscript that will be published in the PLOS journal. In our work, we use the Visual Coding - Neuropixels dataset (Visual Coding Neuropixels - brain-map.org), including recorded mou… --- ## [Finding mouse info (age, sex, strain, genotype etc)](https://community.brain-map.org/t/finding-mouse-info-age-sex-strain-genotype-etc/3409)
**Author:** [@AngCamp](https://community.brain-map.org/u/AngCamp)\ **Replies:** 3\ **Last updated:** [June 25, 2024, 5:09pm UTC](https://community.brain-map.org/t/finding-mouse-info-age-sex-strain-genotype-etc/3409 "2024-06-25T17:09:58Z")
I’m working with the allen neuropixels visual behaviour dataset. How can I search a mouses sex, age, genotype, and strain using its session id? --- ## [Connectivity Synaptic Physiology API -- How to access raw electrophysiology signal data](https://community.brain-map.org/t/connectivity-synaptic-physiology-api-how-to-access-raw-electrophysiology-signal-data/3289)
**Author:** [@jyy20422](https://community.brain-map.org/u/jyy20422)\ **Replies:** 1\ **Last updated:** [May 8, 2024, 8:08pm UTC](https://community.brain-map.org/t/connectivity-synaptic-physiology-api-how-to-access-raw-electrophysiology-signal-data/3289 "2024-05-08T20:08:59Z")
Hello All, Is there a way to access the raw electrophysiology signal data (time series data) from the Synaptic Physiology Database? Thanks! --- ## [Accessing the brain region ontology programmatically](https://community.brain-map.org/t/accessing-the-brain-region-ontology-programmatically/3238)
**Author:** [@NathanSkene](https://community.brain-map.org/u/NathanSkene)\ **Replies:** 3\ **Last updated:** [May 7, 2024, 11:03pm UTC](https://community.brain-map.org/t/accessing-the-brain-region-ontology-programmatically/3238 "2024-05-07T23:03:00Z")
Is there any way to programmatically access the ontology used in the Allen’s interactive atlas? That is, to be able to access the tree structure that Dorsal Thalamus is a child of Thalamus, etc Appreciate that the API … --- ## [Mapping raw merfish 'EntityID' label to 'cell\_label' in CCF transformed coordinates](https://community.brain-map.org/t/mapping-raw-merfish-entityid-label-to-cell-label-in-ccf-transformed-coordinates/3225)
**Author:** [@EdR](https://community.brain-map.org/u/EdR)\ **Replies:** 2\ **Last updated:** [May 7, 2024, 3:12pm UTC](https://community.brain-map.org/t/mapping-raw-merfish-entityid-label-to-cell-label-in-ccf-transformed-coordinates/3225 "2024-05-07T15:12:23Z")
Hello, I am trying to determine how the EntityID found in the .parquet file for each of the raw merfish\_output dirs from the Yao et al. 2023 Study (e.g. Index of /aa/79/aa79b8ba5b3add56/609882/1198980026/merfish\_output… --- ## [Why are the superclusters in the ABC Atlas regional, not excitatory or inhibitory?](https://community.brain-map.org/t/why-are-the-superclusters-in-the-abc-atlas-regional-not-excitatory-or-inhibitory/3219)
**Author:** [@InquilineKea](https://community.brain-map.org/u/InquilineKea)\ **Replies:** 1\ **Last updated:** [May 6, 2024, 3:44pm UTC](https://community.brain-map.org/t/why-are-the-superclusters-in-the-abc-atlas-regional-not-excitatory-or-inhibitory/3219 "2024-05-06T15:44:08Z")
eg from the URL Brain Knowledge Platform, the main UMAP superclusters are not in terms of excitatory or inhibitory influence --- ## [Confused about Human Brain MRI Donor name](https://community.brain-map.org/t/confused-about-human-brain-mri-donor-name/3267)
**Author:** [@Julie\_Park](https://community.brain-map.org/u/Julie_Park)\ **Replies:** 2\ **Last updated:** [April 19, 2024, 4:35am UTC](https://community.brain-map.org/t/confused-about-human-brain-mri-donor-name/3267 "2024-04-19T04:35:04Z")
Hi, I’m having a hard time using Human Brain MRI. I’m trying to use MRI with ‘H0351.2002\_normalized\_microarray\_donor10021’ database, but the name on the table on the website and the name at the top of the image do not m… --- ## [Download new Allen Human-mouse-marmoset dataset](https://community.brain-map.org/t/download-new-allen-human-mouse-marmoset-dataset/1303)
**Author:** [@vivek.mahadevan](https://community.brain-map.org/u/vivek.mahadevan)\ **Replies:** 3\ **Last updated:** [April 5, 2024, 3:54pm UTC](https://community.brain-map.org/t/download-new-allen-human-mouse-marmoset-dataset/1303 "2024-04-05T15:54:26Z")
Hello, I am interested in downloading the datasets associated with this study published yesterday Comparative cellular analysis of motor cortex in human, marmoset and mouse | Nature Data availability statement indicate… --- ## [Is there a way to map sulci/gyri based on the Destrieux atlas to more functional areas (e.g. dorsolateral prefrontal cortex)?](https://community.brain-map.org/t/is-there-a-way-to-map-sulci-gyri-based-on-the-destrieux-atlas-to-more-functional-areas-e-g-dorsolateral-prefrontal-cortex/3201)
**Author:** [@lwl96](https://community.brain-map.org/u/lwl96)\ **Replies:** 1\ **Last updated:** [April 2, 2024, 4:11pm UTC](https://community.brain-map.org/t/is-there-a-way-to-map-sulci-gyri-based-on-the-destrieux-atlas-to-more-functional-areas-e-g-dorsolateral-prefrontal-cortex/3201 "2024-04-02T16:11:30Z")
I have data based on the Destrieux atlas but want to identify the functional regions these cover. Is there a specific way to do this? --- ## [How to recontruct 2D ISH slices into 3D voxel data](https://community.brain-map.org/t/how-to-recontruct-2d-ish-slices-into-3d-voxel-data/3171)
**Author:** [@zz1358](https://community.brain-map.org/u/zz1358)\ **Replies:** 1\ **Last updated:** [March 25, 2024, 8:13pm UTC](https://community.brain-map.org/t/how-to-recontruct-2d-ish-slices-into-3d-voxel-data/3171 "2024-03-25T20:13:34Z")
hello, I am currently trying to segment using 3D voxel ISH data from the whole mouse brain. As I know, 3D voxel data is available at 200 micron resolution. But I want 3D voxel ISH data at higher resolution. I am wander… --- ## [Converting Allen mouse brain cell atlas to nifti](https://community.brain-map.org/t/converting-allen-mouse-brain-cell-atlas-to-nifti/3160)
**Author:** [@bdpharmacy](https://community.brain-map.org/u/bdpharmacy)\ **Replies:** 3\ **Last updated:** [March 19, 2024, 4:43pm UTC](https://community.brain-map.org/t/converting-allen-mouse-brain-cell-atlas-to-nifti/3160 "2024-03-19T16:43:52Z")
I am interested in extracting 3D map of MOG (myelin oligodendrocyte glycoprotein) gene available here (ISH Data :: Allen Brain Atlas: Mouse Brain). I want to download whole mouse brain map of MOG gene as 3D and convert … --- ## [What do "is\_injection" and "id" of structure unionizes mean](https://community.brain-map.org/t/what-do-is-injection-and-id-of-structure-unionizes-mean/3139)
**Author:** [@kantkantwuqh](https://community.brain-map.org/u/kantkantwuqh)\ **Replies:** 1\ **Last updated:** [March 18, 2024, 4:29pm UTC](https://community.brain-map.org/t/what-do-is-injection-and-id-of-structure-unionizes-mean/3139 "2024-03-18T16:29:14Z")
I would like to know the why the structure unionzes of a single experiment would have some many results with different “id”. What is the meaning of “id” and what are the differences between these rows in the table? Also… --- ## [What do the parameters "structure\_ids" of mcc.get\_structure\_unionizes mean?](https://community.brain-map.org/t/what-do-the-parameters-structure-ids-of-mcc-get-structure-unionizes-mean/3138)
**Author:** [@kantkantwuqh](https://community.brain-map.org/u/kantkantwuqh)\ **Replies:** 1\ **Last updated:** [March 18, 2024, 4:24pm UTC](https://community.brain-map.org/t/what-do-the-parameters-structure-ids-of-mcc-get-structure-unionizes-mean/3138 "2024-03-18T16:24:53Z")
In the Structure Signal Unionzation part of the MouseConnectivityCache tutorial jupyter notebook: find wild-type injections into primary visual area visp = structure\_tree.get\_structures\_by\_acronym(\[‘VISp’\])\[0\] visp\_ex… --- ## [Matrix with the number of cells of each celltype, found in each mouse brain region](https://community.brain-map.org/t/matrix-with-the-number-of-cells-of-each-celltype-found-in-each-mouse-brain-region/3115)
**Author:** [@NathanSkene](https://community.brain-map.org/u/NathanSkene)\ **Replies:** 2\ **Last updated:** [March 1, 2024, 6:12pm UTC](https://community.brain-map.org/t/matrix-with-the-number-of-cells-of-each-celltype-found-in-each-mouse-brain-region/3115 "2024-03-01T18:12:13Z")
I’m interested in getting a matrix, based on the data from this paper: A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain | Nature I understand that the paper determined the cell t… --- ## [Spinal cord atlas group](https://community.brain-map.org/t/spinal-cord-atlas-group/3100)
**Author:** [@sulli419](https://community.brain-map.org/u/sulli419)\ **Replies:** 0\ **Last updated:** [February 23, 2024, 7:44pm UTC](https://community.brain-map.org/t/spinal-cord-atlas-group/3100 "2024-02-23T19:44:24Z")
Hi, Is there an active group addressing technical questions about the adult mouse spinal cord reference atlases? I asked a couple of questions but no reply—perhaps they were directed to the wrong place. I’m also curio… --- ## [2022 CCFv3 mouse atlas](https://community.brain-map.org/t/2022-ccfv3-mouse-atlas/2287)
**Author:** [@buddjm](https://community.brain-map.org/u/buddjm)\ **Replies:** 6\ **Last updated:** [January 31, 2024, 12:54pm UTC](https://community.brain-map.org/t/2022-ccfv3-mouse-atlas/2287 "2024-01-31T12:54:02Z")
Hi, Please can you refer me to any documentation/publications regarding the creation of the 2022 adult mouse CCFv3 annotation atlas (only available at 10 um voxel resolution) that includes many new layer annotations: se… --- ## [Code to visualize neuropixel probe trajectories from the visual behaviour dataset?](https://community.brain-map.org/t/code-to-visualize-neuropixel-probe-trajectories-from-the-visual-behaviour-dataset/2943)
**Author:** [@AngCamp](https://community.brain-map.org/u/AngCamp)\ **Replies:** 6\ **Last updated:** [January 26, 2024, 10:27pm UTC](https://community.brain-map.org/t/code-to-visualize-neuropixel-probe-trajectories-from-the-visual-behaviour-dataset/2943 "2024-01-26T22:27:32Z")
Hello is there a notebook somewhere that can be used to make a figure showing the trajectory of probes through the brain for the visual behaviour neuropixels dataset? --- ## [Question about coregistering mouse brain ABA\_V3 to 3D data; especially pertaining to region labels](https://community.brain-map.org/t/question-about-coregistering-mouse-brain-aba-v3-to-3d-data-especially-pertaining-to-region-labels/2901)
**Author:** [@liamm](https://community.brain-map.org/u/liamm)\ **Replies:** 1\ **Last updated:** [January 18, 2024, 6:03pm UTC](https://community.brain-map.org/t/question-about-coregistering-mouse-brain-aba-v3-to-3d-data-especially-pertaining-to-region-labels/2901 "2024-01-18T18:03:45Z")
I am trying to use the AVA\_V3 atlas downloaded from here: https://scalablebrainatlas.incf.org/mouse/ABA\_v3 to coregister region labels onto my own 3D mouse brain data. I did download the annotated .nii atlas and noticed… --- ## [Donor information - cause of death, healthy donors?](https://community.brain-map.org/t/donor-information-cause-of-death-healthy-donors/2909)
**Author:** [@ksiemens](https://community.brain-map.org/u/ksiemens)\ **Replies:** 1\ **Last updated:** [January 16, 2024, 7:51pm UTC](https://community.brain-map.org/t/donor-information-cause-of-death-healthy-donors/2909 "2024-01-16T19:51:47Z")
I am looking for information on the donors used in the microarray dataset (H0351.2001, H0351.2002, H0351,1009, H0351.1012, H0351.1015, H0351.1016). I see the age, sex, ethnicity and PMI. Is there any further information… --- ## [Merfish gene panel](https://community.brain-map.org/t/merfish-gene-panel/2821)
**Author:** [@susant](https://community.brain-map.org/u/susant)\ **Replies:** 5\ **Last updated:** [January 10, 2024, 7:03pm UTC](https://community.brain-map.org/t/merfish-gene-panel/2821 "2024-01-10T19:03:41Z")
I’m wondering why the file (cl.df\_CCN202307220.xls, tab- MERFISH GENE PANEL) posted under the link “Whole adult mouse brain taxonomy of cell types” only lists ~500 genes, when the Zhang et al paper mentions \>1000, as doe… --- ## [Can't access mouse ISH brain atlas documentation](https://community.brain-map.org/t/cant-access-mouse-ish-brain-atlas-documentation/2784)
**Author:** [@d45ha](https://community.brain-map.org/u/d45ha)\ **Replies:** 5\ **Last updated:** [January 9, 2024, 6:45pm UTC](https://community.brain-map.org/t/cant-access-mouse-ish-brain-atlas-documentation/2784 "2024-01-09T18:45:25Z")
Hi, I’m struggling to access the ‘Documentation’ or ‘Help’ pages for the mouse brain ISH atlas. I keep getting a webpage saying the site is down for maintenance. I was hoping to use some data for my PhD project and am wo… --- ## [Atlas ROI parcellation](https://community.brain-map.org/t/atlas-roi-parcellation/2825)
**Author:** [@SAA](https://community.brain-map.org/u/SAA)\ **Replies:** 0\ **Last updated:** [January 3, 2024, 3:21am UTC](https://community.brain-map.org/t/atlas-roi-parcellation/2825 "2024-01-03T03:21:49Z")
Hello, I’m new to this area. I have register my own mouse data to Allen p56 atlas, and I just want to analyze some result in few of mouse brain areas. But the problem I met is that I cannot find a direct way to download … --- ## [Median value of channels subtracted to denoise in Neuropixels dataset](https://community.brain-map.org/t/median-value-of-channels-subtracted-to-denoise-in-neuropixels-dataset/2773)
**Author:** [@Jsl](https://community.brain-map.org/u/Jsl)\ **Replies:** 3\ **Last updated:** [December 12, 2023, 4:24pm UTC](https://community.brain-map.org/t/median-value-of-channels-subtracted-to-denoise-in-neuropixels-dataset/2773 "2023-12-12T16:24:23Z")
Hi, I read from the white paper that "For each sample, the median value of channels N:24:384, where N = \[1,2,3,…,24\], was calculated, and this value was subtracted from the same set of channels. " Is this why some nega… --- ## [Calculating CSD](https://community.brain-map.org/t/calculating-csd/2724)
**Author:** [@paxpoggi](https://community.brain-map.org/u/paxpoggi)\ **Replies:** 1\ **Last updated:** [November 29, 2023, 7:01pm UTC](https://community.brain-map.org/t/calculating-csd/2724 "2023-11-29T19:01:13Z")
Hi, I am trying to calculate CSD data for all presentation types based on the LFP data. I am having trouble figuring out how to align the lfp channels based on their vertical and horizontal positions because there are 1/… --- ## [Where can I find the mouse brain images with fluorescence in situ hybridization (FISH)? Do you also have the protocol of FISH?](https://community.brain-map.org/t/where-can-i-find-the-mouse-brain-images-with-fluorescence-in-situ-hybridization-fish-do-you-also-have-the-protocol-of-fish/2726)
**Author:** [@Chen\_Z](https://community.brain-map.org/u/Chen_Z)\ **Replies:** 0\ **Last updated:** [November 27, 2023, 3:11pm UTC](https://community.brain-map.org/t/where-can-i-find-the-mouse-brain-images-with-fluorescence-in-situ-hybridization-fish-do-you-also-have-the-protocol-of-fish/2726 "2023-11-27T15:11:22Z")
Hello, I am working on a project investigating the gene of interest in different regions in mouse brain. Before I start with FISH, I would like to know the expression of the gene of interest throughout the whole brain. … --- ## [Missing LFP channels, and scale factor](https://community.brain-map.org/t/missing-lfp-channels-and-scale-factor/2706)
**Author:** [@AngCamp](https://community.brain-map.org/u/AngCamp)\ **Replies:** 3\ **Last updated:** [November 20, 2023, 7:25pm UTC](https://community.brain-map.org/t/missing-lfp-channels-and-scale-factor/2706 "2023-11-20T19:25:54Z")
I have been working with the LFP data from the Allen Institute Neuropixels Visual Behaviour dataset. I have two questions about working with the LFP data. 1) Scale factor Firstly in the tutorial on LFP analysis (here) … --- ## [Trouble using API to download SVG image of Mouse brain sagittal section](https://community.brain-map.org/t/trouble-using-api-to-download-svg-image-of-mouse-brain-sagittal-section/2713)
**Author:** [@AlexE19INP](https://community.brain-map.org/u/AlexE19INP)\ **Replies:** 0\ **Last updated:** [November 17, 2023, 7:57pm UTC](https://community.brain-map.org/t/trouble-using-api-to-download-svg-image-of-mouse-brain-sagittal-section/2713 "2023-11-17T19:57:04Z")
Before starting, I just want to mention I have no background in coding/XML and so I’ve first tried using the SDK but I can’t seem to get that to work, and so would like a thorough explanation of either how to use the SDK… --- ## [Differences in z-score values for the same donor, same probe and same region](https://community.brain-map.org/t/differences-in-z-score-values-for-the-same-donor-same-probe-and-same-region/2691)
**Author:** [@Sdh](https://community.brain-map.org/u/Sdh)\ **Replies:** 3\ **Last updated:** [November 13, 2023, 12:56pm UTC](https://community.brain-map.org/t/differences-in-z-score-values-for-the-same-donor-same-probe-and-same-region/2691 "2023-11-13T12:56:51Z")
I tried looking for z-scores values on Allen brain atlas (on the six healthy brain donors). Does anyone know why z-score values are different when you look at them on the two screen shots? These values are for the same … [Previous page](https://community.brain-map.org/c/general/1.md?page=3) [Next page](https://community.brain-map.org/c/general/1.md?page=5)