# \#api **URL:** https://community.brain-map.org/tag/api/43.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) --- ## [Is human microarray expression service down/deprecated?](https://community.brain-map.org/t/is-human-microarray-expression-service-down-deprecated/4009)
**Author:** [@AhmetN](https://community.brain-map.org/u/AhmetN)\ **Replies:** 6\ **Last updated:** [June 30, 2026, 5:25am UTC](https://community.brain-map.org/t/is-human-microarray-expression-service-down-deprecated/4009 "2026-06-30T05:25:12Z")
Dear Allen Team, I have been using the allen api (https://api.brain-map.org/api/v2) and human\_microarray\_expression service as described here Human Brain Atlas: API. However, for about a month now, my queries to the hum… --- ## [Visual Degrees to Pixels Mapping Convention](https://community.brain-map.org/t/visual-degrees-to-pixels-mapping-convention/4964)
**Author:** [@basementcrusader](https://community.brain-map.org/u/basementcrusader)\ **Replies:** 1\ **Last updated:** [June 15, 2026, 6:52pm UTC](https://community.brain-map.org/t/visual-degrees-to-pixels-mapping-convention/4964 "2026-06-15T18:52:58Z")
Hi, I am using some gaze mapping data from a visual coding experiment to understand the center of gaze during a stimulus presentation. I have included an example of my code below calculating the gazePosition on the moni… --- ## [Programmatic download of human ISH - issues with allensdk](https://community.brain-map.org/t/programmatic-download-of-human-ish-issues-with-allensdk/4846)
**Author:** [@MPanday](https://community.brain-map.org/u/MPanday)\ **Replies:** 2\ **Last updated:** [March 25, 2026, 3:36pm UTC](https://community.brain-map.org/t/programmatic-download-of-human-ish-issues-with-allensdk/4846 "2026-03-25T15:36:54Z")
Hello @SvenOtto @racheld @tylermo I am planning a study that uses a large amount of ISH data from the human database and was wondering how I could retrieve that data programmatically (autism study). I know there’s a pyt… --- ## [Discrepancies between connectivity data retrieved via API (allenSDK) and the web portal](https://community.brain-map.org/t/discrepancies-between-connectivity-data-retrieved-via-api-allensdk-and-the-web-portal/3766)
**Author:** [@DavideR](https://community.brain-map.org/u/DavideR)\ **Replies:** 1\ **Last updated:** [March 25, 2026, 3:10pm UTC](https://community.brain-map.org/t/discrepancies-between-connectivity-data-retrieved-via-api-allensdk-and-the-web-portal/3766 "2026-03-25T15:10:49Z")
Hi, I’d like to retrieve, via API, the connectivity data for a given target structure, but I had some issues and I don’t know if I’m doing the correct process. The example in the Jupyter notebook “Introduction to the Mo… --- ## [Allenbrain-mcp — MCP server wrapper for Allen Brain Atlas API (RMA + downloads)](https://community.brain-map.org/t/allenbrain-mcp-mcp-server-wrapper-for-allen-brain-atlas-api-rma-downloads/4858)
**Author:** [@maflot](https://community.brain-map.org/u/maflot)\ **Replies:** 0\ **Last updated:** [February 25, 2026, 3:53pm UTC](https://community.brain-map.org/t/allenbrain-mcp-mcp-server-wrapper-for-allen-brain-atlas-api-rma-downloads/4858 "2026-02-25T15:53:58Z")
Request for feedback: allenbrain-mcp (MCP wrapper for the Allen Brain Atlas API) + worked C4b example Hello everyone, I have been developing a small Model Context Protocol (MCP) server that exposes a curated subset of t… --- ## [Question on PatchSeq jupyter example](https://community.brain-map.org/t/question-on-patchseq-jupyter-example/1030)
**Author:** [@eblf](https://community.brain-map.org/u/eblf)\ **Replies:** 10\ **Last updated:** [October 22, 2025, 6:56am UTC](https://community.brain-map.org/t/question-on-patchseq-jupyter-example/1030 "2025-10-22T06:56:48Z")
Straightforward q: in the example jupyter notebook from the Multimodal Characterization in Mouse Visual Cortex where is the select\_markers.csv file or do you have an example of information needed to create my own similar… --- ## [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… --- ## [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… --- ## [Programmatically accessing Human ISH](https://community.brain-map.org/t/programmatically-accessing-human-ish/4171)
**Author:** [@MPanday](https://community.brain-map.org/u/MPanday)\ **Replies:** 2\ **Last updated:** [May 20, 2025, 7:04pm UTC](https://community.brain-map.org/t/programmatically-accessing-human-ish/4171 "2025-05-20T19:04:34Z")
Hi there, I’m working with the Allen Human Brain ISH database, and I’m trying to retrieve large amounts of image data for a neuroanatomy project involving cell morphologies. I know from my previous work with the mouse … --- ## [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… --- ## [How to download images from the Ivy Glioblastoma Atlas Project](https://community.brain-map.org/t/how-to-download-images-from-the-ivy-glioblastoma-atlas-project/215)
**Author:** [@wayne](https://community.brain-map.org/u/wayne)\ **Replies:** 3\ **Last updated:** [January 7, 2025, 11:04pm UTC](https://community.brain-map.org/t/how-to-download-images-from-the-ivy-glioblastoma-atlas-project/215 "2025-01-07T23:04:15Z")
I’m trying to download all the images on IvyGAP (ISH, H&E, TumorFeature). I was able to locate the APIs page (http://help.brain-map.org/display/glioblastoma/API), but it seems that this either has to be done through webs… --- ## [Human.brain-map.org can't be reached](https://community.brain-map.org/t/human-brain-map-org-cant-be-reached/3921)
**Author:** [@xubingjie](https://community.brain-map.org/u/xubingjie)\ **Replies:** 4\ **Last updated:** [December 4, 2024, 1:46pm UTC](https://community.brain-map.org/t/human-brain-map-org-cant-be-reached/3921 "2024-12-04T13:46:29Z")
I am using the get\_samples\_in\_mask function from the abagen to access data from the Allen Human Brain Atlas (AHBA), but I am unable to access https://human.brain-map.org/api/v2/well\_known\_file\_download/178238387. Where c… --- ## [Error downloading images via Atlas ID](https://community.brain-map.org/t/error-downloading-images-via-atlas-id/3933)
**Author:** [@EShunter](https://community.brain-map.org/u/EShunter)\ **Replies:** 0\ **Last updated:** [December 3, 2024, 7:16am UTC](https://community.brain-map.org/t/error-downloading-images-via-atlas-id/3933 "2024-12-03T07:16:09Z")
Hello，I noticed that when downloading images via atlas ID, as following http://api.brain-map.org/api/v2/data/query.xml?criteria=model::AtlasImage, rma::criteria, \[annotated$eqtrue\],atlas\_data\_set(atlases\[id$eq2\]),altern… --- ## [Problem on accessing NWB files in BrainObservatory Cache](https://community.brain-map.org/t/problem-on-accessing-nwb-files-in-brainobservatory-cache/3911)
**Author:** [@CRYPTOCHROME384](https://community.brain-map.org/u/CRYPTOCHROME384)\ **Replies:** 5\ **Last updated:** [December 3, 2024, 2:09am UTC](https://community.brain-map.org/t/problem-on-accessing-nwb-files-in-brainobservatory-cache/3911 "2024-12-03T02:09:12Z")
Hi everyone, It’s really cool of you guys to share all these data online. I am currently working on the VIsp’s 2P data, here’s my code to download the original nwb files on my server: from allensdk.core.brain\_observato… --- ## [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… --- ## [API issue with oapi.get\_structures\_with\_sets?](https://community.brain-map.org/t/api-issue-with-oapi-get-structures-with-sets/2357)
**Author:** [@pderdeyn](https://community.brain-map.org/u/pderdeyn)\ **Replies:** 5\ **Last updated:** [July 19, 2024, 8:15pm UTC](https://community.brain-map.org/t/api-issue-with-oapi-get-structures-with-sets/2357 "2024-07-19T20:15:20Z")
I’m having an issue running some code from the AllenSDK (JSONDecodeError when running oapi.get\_structures\_with\_sets(\[1\]) · Issue #2684 · AllenInstitute/AllenSDK · GitHub). I get a JSONDecodeError when trying to run the f… --- ## [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 directory of SectionImage](https://community.brain-map.org/t/accessing-directory-of-sectionimage/3230)
**Author:** [@rdaggs27](https://community.brain-map.org/u/rdaggs27)\ **Replies:** 0\ **Last updated:** [April 4, 2024, 6:25pm UTC](https://community.brain-map.org/t/accessing-directory-of-sectionimage/3230 "2024-04-04T18:25:30Z")
Hello all – I am a newcomer to this dataset and am working with the Image-to-Atlas and Image-to-Image API and I wanted someone’s advice. I have a dataset of coronal scans and am looking to overlay atlas-based subregions … --- ## [Human Reference Atlas Right Hemisphere](https://community.brain-map.org/t/human-reference-atlas-right-hemisphere/595)
**Author:** [@jopeter](https://community.brain-map.org/u/jopeter)\ **Replies:** 2\ **Last updated:** [March 8, 2024, 11:12am UTC](https://community.brain-map.org/t/human-reference-atlas-right-hemisphere/595 "2024-03-08T11:12:20Z")
Hello, Do there exist files for the right hemisphere of the human reference atlas? Thanks, Jonah --- ## [Is it possible to pull data into Google Cloud Storage from AllenSDK API directly from a cloud notebook instance?](https://community.brain-map.org/t/is-it-possible-to-pull-data-into-google-cloud-storage-from-allensdk-api-directly-from-a-cloud-notebook-instance/2611)
**Author:** [@mariakesa](https://community.brain-map.org/u/mariakesa)\ **Replies:** 1\ **Last updated:** [October 9, 2023, 5:16pm UTC](https://community.brain-map.org/t/is-it-possible-to-pull-data-into-google-cloud-storage-from-allensdk-api-directly-from-a-cloud-notebook-instance/2611 "2023-10-09T17:16:17Z")
My computer is about 7 years old. It’s great it has a GPU and SSD, but it’s not enough for a holiday project that I came up with. I ran up against a wall for the data storage and processing power I need. I need cloud co… --- ## [How to construct an API that would contain a white space within the name of a brain structure - SOLVED](https://community.brain-map.org/t/how-to-construct-an-api-that-would-contain-a-white-space-within-the-name-of-a-brain-structure-solved/2580)
**Author:** [@Faustino](https://community.brain-map.org/u/Faustino)\ **Replies:** 0\ **Last updated:** [September 10, 2023, 5:02pm UTC](https://community.brain-map.org/t/how-to-construct-an-api-that-would-contain-a-white-space-within-the-name-of-a-brain-structure-solved/2580 "2023-09-10T17:02:09Z")
I would like to build an API equivalent to this one, offered as an example in the API section of the Allen Brain web: http://api.brain-map.org/api/v2/data/query.json?criteria=service::mouse\_connectivity\_injection\_struct… --- ## [Is the absolute soma depth (in um) available for the neurons in the Cell Types database?](https://community.brain-map.org/t/is-the-absolute-soma-depth-in-um-available-for-the-neurons-in-the-cell-types-database/1748)
**Author:** [@Thijs](https://community.brain-map.org/u/Thijs)\ **Replies:** 8\ **Last updated:** [July 14, 2023, 8:24am UTC](https://community.brain-map.org/t/is-the-absolute-soma-depth-in-um-available-for-the-neurons-in-the-cell-types-database/1748 "2023-07-14T08:24:31Z")
Hi, I would like to have the absolute distance of the soma from pia for some of the neurons in the cell types database. Is this available? I’ve so far only found nomalised soma depth. From the Kalmbach et al Neuron 2018 … --- ## [Is there a way to check which brains have been annotated using the API?](https://community.brain-map.org/t/is-there-a-way-to-check-which-brains-have-been-annotated-using-the-api/2424)
**Author:** [@moldenha](https://community.brain-map.org/u/moldenha)\ **Replies:** 1\ **Last updated:** [June 23, 2023, 5:15pm UTC](https://community.brain-map.org/t/is-there-a-way-to-check-which-brains-have-been-annotated-using-the-api/2424 "2023-06-23T17:15:25Z")
I am trying to do a study about variability in mice brains, and was wondering if there was a way to check which brains have been annotated. The only one that I have seen that has been coronally sectioned and annotated wa… --- ## [Differences in Hex Values for Brain Regions Across Different Sources](https://community.brain-map.org/t/differences-in-hex-values-for-brain-regions-across-different-sources/2401)
**Author:** [@yelgreb\_nelg](https://community.brain-map.org/u/yelgreb_nelg)\ **Replies:** 0\ **Last updated:** [June 14, 2023, 7:09pm UTC](https://community.brain-map.org/t/differences-in-hex-values-for-brain-regions-across-different-sources/2401 "2023-06-14T19:09:32Z")
Hi everyone, While developing an SVG-based visualizer, I’ve noticed that the Scalable Brain Atlas and the Allen Brain Atlas API use different hexadecimal values to represent the same brain regions. For example, this JS… --- ## [API connection issues](https://community.brain-map.org/t/api-connection-issues/2348)
**Author:** [@spraguedawley](https://community.brain-map.org/u/spraguedawley)\ **Replies:** 0\ **Last updated:** [May 20, 2023, 12:01pm UTC](https://community.brain-map.org/t/api-connection-issues/2348 "2023-05-20T12:01:26Z")
Hi everyone, I have been using the API for the last week and I have experienced that the connection gets interrupted quite often. May this be related to some server issues or are there any API limits (# of queries per s… --- ## [Downlaod recording metadata only](https://community.brain-map.org/t/downlaod-recording-metadata-only/2255)
**Author:** [@arashgmn](https://community.brain-map.org/u/arashgmn)\ **Replies:** 2\ **Last updated:** [April 5, 2023, 1:04pm UTC](https://community.brain-map.org/t/downlaod-recording-metadata-only/2255 "2023-04-05T13:04:58Z")
Hi, I was wondering if there’s a way to download only the recording metadata without downloading the entire “medium” synaptic physiology dataset; Or even better, is there a sample/metadata of such metadata? I have bandw… --- ## [Trying to get a complete list of all the ISH ID experiments for the mouse brain](https://community.brain-map.org/t/trying-to-get-a-complete-list-of-all-the-ish-id-experiments-for-the-mouse-brain/2089)
**Author:** [@spiluso](https://community.brain-map.org/u/spiluso)\ **Replies:** 3\ **Last updated:** [March 16, 2023, 6:47pm UTC](https://community.brain-map.org/t/trying-to-get-a-complete-list-of-all-the-ish-id-experiments-for-the-mouse-brain/2089 "2023-03-16T18:47:05Z")
Hi, I was just wondering how to easily get a complete list of all the ISH ID experiments for the mouse brain. I have tried different ways through API queries but it is difficult to get the complete list because ID figu… --- ## [36 reconstructed mouse GABA neurons cannot be accessed](https://community.brain-map.org/t/36-reconstructed-mouse-gaba-neurons-cannot-be-accessed/2003)
**Author:** [@fun0515](https://community.brain-map.org/u/fun0515)\ **Replies:** 6\ **Last updated:** [January 6, 2023, 11:50am UTC](https://community.brain-map.org/t/36-reconstructed-mouse-gaba-neurons-cannot-be-accessed/2003 "2023-01-06T11:50:28Z")
I’m now trying to download the available 528 reconstructed neuron data opened by an article in the BICCN project, titled “Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells”(Multimoda… [Next page](https://community.brain-map.org/tag/api/43.md?match_all_tags=true&page=1&tags%5B%5D=api)