# \#software **URL:** https://community.brain-map.org/tag/software/69.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) --- ## [Issue with MapMyCells website?](https://community.brain-map.org/t/issue-with-mapmycells-website/5053)
**Author:** [@jungeji99](https://community.brain-map.org/u/jungeji99)\ **Replies:** 4\ **Last updated:** [September 1, 2026, 8:26pm UTC](https://community.brain-map.org/t/issue-with-mapmycells-website/5053 "2026-09-01T20:26:59Z")
Hello. I am currently bumping into an issue where a message of 'Mapping Failed’is popping up. I was wondering if it might be caused by an internal change in the website, as this issue is occurring for datasets that I hav… --- ## [Allen Reference Atlas](https://community.brain-map.org/t/allen-reference-atlas/4913)
**Author:** [@abbytlong](https://community.brain-map.org/u/abbytlong)\ **Replies:** 1\ **Last updated:** [June 3, 2026, 3:56am UTC](https://community.brain-map.org/t/allen-reference-atlas/4913 "2026-06-03T03:56:40Z")
Hello, I have tried to access the Allen brain atlas for the coronal reference atlas, and have not successfully opened the page on any device I have tried to open it on. I have attached the message I receive when I press … --- ## [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… --- ## [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… --- ## [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… --- ## [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… --- ## [Mouse brain volume from software](https://community.brain-map.org/t/mouse-brain-volume-from-software/4204)
**Author:** [@Natt](https://community.brain-map.org/u/Natt)\ **Replies:** 2\ **Last updated:** [March 4, 2025, 8:54am UTC](https://community.brain-map.org/t/mouse-brain-volume-from-software/4204 "2025-03-04T08:54:19Z")
Hi everyone, First of all, I want to express my gratitude for the incredible work that has gone into creating the Allen Brain Map. The resources and tools provided are truly invaluable. Thank you! I’ve been exploring t… --- ## [Brain Explorer on Mac Catalina](https://community.brain-map.org/t/brain-explorer-on-mac-catalina/558)
**Author:** [@sofia.grade](https://community.brain-map.org/u/sofia.grade)\ **Replies:** 6\ **Last updated:** [December 21, 2024, 1:00am UTC](https://community.brain-map.org/t/brain-explorer-on-mac-catalina/558 "2024-12-21T01:00:02Z")
Brain Explorer is not working well on my new MacBook. My laptop fulfils the minimum requirements but when I open Brain Explorer 1) the structures are listed but cannot be visualised when I select the structure(s), nothin… --- ## [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… --- ## [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? --- ## [How do I download specific cell type gene expression data from WHB?](https://community.brain-map.org/t/how-do-i-download-specific-cell-type-gene-expression-data-from-whb/3648)
**Author:** [@atown](https://community.brain-map.org/u/atown)\ **Replies:** 2\ **Last updated:** [September 9, 2024, 6:34pm UTC](https://community.brain-map.org/t/how-do-i-download-specific-cell-type-gene-expression-data-from-whb/3648 "2024-09-09T18:34:58Z")
Thank you for the Allen Brain cell atlas data access tool! Is there a way to download a subset of the gene expression raw data? For example, looking at a specific cell type of interest such as Astrocytes. I saw that you … --- ## [MERFISH Imputed Genes Now Available through abc\_atlas\_access](https://community.brain-map.org/t/merfish-imputed-genes-now-available-through-abc-atlas-access/3587)
**Author:** [@morriscb](https://community.brain-map.org/u/morriscb)\ **Replies:** 0\ **Last updated:** [August 19, 2024, 9:51pm UTC](https://community.brain-map.org/t/merfish-imputed-genes-now-available-through-abc-atlas-access/3587 "2024-08-19T21:51:24Z")
Hi everyone, We’ve released an update to the abc\_atlas\_access package. This update adds the MERFISH imputed gene data created in Yao et al., adding more than 8k genes to the MERFISH dataset. You can find more details in… --- ## [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 --- ## [NWB Schema Version For Multimodal Characterization in Mouse Visual Cortex](https://community.brain-map.org/t/nwb-schema-version-for-multimodal-characterization-in-mouse-visual-cortex/866)
**Author:** [@dynsys](https://community.brain-map.org/u/dynsys)\ **Replies:** 3\ **Last updated:** [January 28, 2024, 10:38pm UTC](https://community.brain-map.org/t/nwb-schema-version-for-multimodal-characterization-in-mouse-visual-cortex/866 "2024-01-28T22:38:45Z")
I understand from reading the community forum that you do not support MATLAB reading of NWB files, but I am wondering the following, so that I can fix my own problem. The intracellular ephys data for the Multimodal Char… --- ## [Time vector for spike waveform averages in Brain Observatory datasets](https://community.brain-map.org/t/time-vector-for-spike-waveform-averages-in-brain-observatory-datasets/2355)
**Author:** [@stankov](https://community.brain-map.org/u/stankov)\ **Replies:** 7\ **Last updated:** [May 26, 2023, 11:20am UTC](https://community.brain-map.org/t/time-vector-for-spike-waveform-averages-in-brain-observatory-datasets/2355 "2023-05-26T11:20:17Z")
Hi everyone. Does anyone know the time vector concerning the average waveforms that out made by Kilosort2 for the Brain Observatory datasets for the visual and resting state animals (~58 animals in total)? Also is there … --- ## [Hello, may I know your backend storage architecture for data and your solution for displaying image data in the browser?](https://community.brain-map.org/t/hello-may-i-know-your-backend-storage-architecture-for-data-and-your-solution-for-displaying-image-data-in-the-browser/2340)
**Author:** [@xuwenhao2525](https://community.brain-map.org/u/xuwenhao2525)\ **Replies:** 0\ **Last updated:** [May 6, 2023, 1:21pm UTC](https://community.brain-map.org/t/hello-may-i-know-your-backend-storage-architecture-for-data-and-your-solution-for-displaying-image-data-in-the-browser/2340 "2023-05-06T13:21:06Z")
Because my current academic topic involves the storage management and visualization of the TCM image data of the research group, I would like to use your design model for reference. Is there any related technical documen… --- ## [Advanced Notice: End-of-life for Allen Brain Explorer (desktop app)](https://community.brain-map.org/t/advanced-notice-end-of-life-for-allen-brain-explorer-desktop-app/575)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 2\ **Last updated:** [March 3, 2023, 7:50pm UTC](https://community.brain-map.org/t/advanced-notice-end-of-life-for-allen-brain-explorer-desktop-app/575 "2023-03-03T19:50:54Z")
Dear community members, Due to technical considerations and competing priorities, the Allen Institute plans to retire the desktop Allen Brain Explorer application by mid 2021, roughly 12 months from now. Much of the fu… --- ## [Number of detections in parent object not always the sum of number of detections in child objects](https://community.brain-map.org/t/number-of-detections-in-parent-object-not-always-the-sum-of-number-of-detections-in-child-objects/2108)
**Author:** [@tvulli](https://community.brain-map.org/u/tvulli)\ **Replies:** 4\ **Last updated:** [January 30, 2023, 10:00pm UTC](https://community.brain-map.org/t/number-of-detections-in-parent-object-not-always-the-sum-of-number-of-detections-in-child-objects/2108 "2023-01-30T22:00:03Z")
Hello everyone, I am currently wondering why the summation of the DAPI detected cells via stardist in the ventricular systems (1157), fiber tracts (13868), and basic cell groups and regions (160543) objects in the attac… --- ## [Datajoint Database for Microns Functional Data](https://community.brain-map.org/t/datajoint-database-for-microns-functional-data/1813)
**Author:** [@hisannaeem](https://community.brain-map.org/u/hisannaeem)\ **Replies:** 1\ **Last updated:** [August 22, 2022, 3:10pm UTC](https://community.brain-map.org/t/datajoint-database-for-microns-functional-data/1813 "2022-08-22T15:10:18Z")
Hello, I am a student researcher looking into the Microns dataset. I was able to explore the synaptic data, and I am looking for a hosted version of the functional data database as well, similar to the synapses data. I s… --- ## [File download format](https://community.brain-map.org/t/file-download-format/1745)
**Author:** [@GerrikLabra](https://community.brain-map.org/u/GerrikLabra)\ **Replies:** 2\ **Last updated:** [August 18, 2022, 2:45pm UTC](https://community.brain-map.org/t/file-download-format/1745 "2022-08-18T14:45:10Z")
For the expression, probe, and columns files when downloading the microarray data from the Web Portal for gene classes, or differential searches, could the files be in .txt or .csv format? Currently they are in Microsoft… --- ## [Some questions about Mouse Brain Atlas in Brain Explorer 2](https://community.brain-map.org/t/some-questions-about-mouse-brain-atlas-in-brain-explorer-2/1672)
**Author:** [@WThainan](https://community.brain-map.org/u/WThainan)\ **Replies:** 1\ **Last updated:** [June 21, 2022, 10:27pm UTC](https://community.brain-map.org/t/some-questions-about-mouse-brain-atlas-in-brain-explorer-2/1672 "2022-06-21T22:27:00Z")
I have some questions on Brain Explorer 2.I want to know what is the template of allen mouse brain atlas and how to define the structures in mouse brain? If have some documents or literatures that explain related issue… --- ## [Projection detection module](https://community.brain-map.org/t/projection-detection-module/1394)
**Author:** [@Antorhythms](https://community.brain-map.org/u/Antorhythms)\ **Replies:** 1\ **Last updated:** [January 20, 2022, 4:20pm UTC](https://community.brain-map.org/t/projection-detection-module/1394 "2022-01-20T16:20:11Z")
Hi, I was wondering if the code of the projection detection module referenced in the TECHNICAL WHITE PAPER:INFORMATICS DATA PROCESSING is shared anywhere. The white paper reads : “The image was transformed using the sq… --- ## [Marker genes of Transcriptomic explorer](https://community.brain-map.org/t/marker-genes-of-transcriptomic-explorer/1328)
**Author:** [@nmeo](https://community.brain-map.org/u/nmeo)\ **Replies:** 1\ **Last updated:** [November 9, 2021, 9:22pm UTC](https://community.brain-map.org/t/marker-genes-of-transcriptomic-explorer/1328 "2021-11-09T21:22:21Z")
Hi, I’m trying to identify marker genes for each cell cluster in “multiple cortical areas” snRNA data sets, It would be great if you could help me with the following questions: What was the algorithm for selecting t… --- ## [OpenScope Applicant Webinar - ask your follow-up questions](https://community.brain-map.org/t/openscope-applicant-webinar-ask-your-follow-up-questions/1275)
**Author:** [@kaitlync](https://community.brain-map.org/u/kaitlync)\ **Replies:** 0\ **Last updated:** [September 13, 2021, 6:43pm UTC](https://community.brain-map.org/t/openscope-applicant-webinar-ask-your-follow-up-questions/1275 "2021-09-13T18:43:52Z")
We held the OpenScope Applicant Webinar on Monday, September 13, to provide guidance to prospective applicants to the OpenScope program. The webinar was recorded and can be watched here. The 2021 RFP is due September 22. … --- ## [Visual Behavior - Optical Physiology](https://community.brain-map.org/t/visual-behavior-optical-physiology/1183)
**Author:** [@oamine](https://community.brain-map.org/u/oamine)\ **Replies:** 4\ **Last updated:** [July 13, 2021, 6:17pm UTC](https://community.brain-map.org/t/visual-behavior-optical-physiology/1183 "2021-07-13T18:17:01Z")
Hello, We are trying to download a specific performance metric across all of the mice who went through a specific experiment type, say OPHYS\_1\_images\_A. The jupyter notebooks provided with the AllenSDK are very helpful … --- ## [Find ISH data related to specific atlas plate](https://community.brain-map.org/t/find-ish-data-related-to-specific-atlas-plate/1078)
**Author:** [@mkunst23](https://community.brain-map.org/u/mkunst23)\ **Replies:** 3\ **Last updated:** [May 28, 2021, 8:28pm UTC](https://community.brain-map.org/t/find-ish-data-related-to-specific-atlas-plate/1078 "2021-05-28T20:28:03Z")
I’m trying to download ISH section for a specific region of the brain. Is there a function in the allenSDK to find the image of an ISH experiment that is closest a specific location in the atlas? I found the image\_to\_at… --- ## [Can't open session .nwb files on Matlab or Python](https://community.brain-map.org/t/cant-open-session-nwb-files-on-matlab-or-python/464)
**Author:** [@eabhorrocks](https://community.brain-map.org/u/eabhorrocks)\ **Replies:** 10\ **Last updated:** [April 22, 2021, 10:38pm UTC](https://community.brain-map.org/t/cant-open-session-nwb-files-on-matlab-or-python/464 "2021-04-22T22:38:25Z")
I’m trying to open visual-coding neuropixel .nwb files using both Python and Matlab using pynwb and matnwb. When I try and open the session .nwb files I get the following errors: Python I’m new to using .nwb files but … --- ## [Cannot download gene expression profiles and see 'structure' window](https://community.brain-map.org/t/cannot-download-gene-expression-profiles-and-see-structure-window/994)
**Author:** [@Jabbott7](https://community.brain-map.org/u/Jabbott7)\ **Replies:** 1\ **Last updated:** [March 18, 2021, 7:59pm UTC](https://community.brain-map.org/t/cannot-download-gene-expression-profiles-and-see-structure-window/994 "2021-03-18T19:59:33Z")
Hi, I am having some issues with all of my downloaded Allan Brain Atlases on my Windows laptop. As you can see in the images attached, I find it very difficult to navigate the ‘Structure’ tab as it seems to no be fully … --- ## [Alternative Synapse Models in BMTK](https://community.brain-map.org/t/alternative-synapse-models-in-bmtk/920)
**Author:** [@Jonasver](https://community.brain-map.org/u/Jonasver)\ **Replies:** 1\ **Last updated:** [February 1, 2021, 5:07pm UTC](https://community.brain-map.org/t/alternative-synapse-models-in-bmtk/920 "2021-02-01T17:07:26Z")
Hi all, Does anyone know if there are any short-term dynamic synaptic models available for point-net in BMTK? Is there an overview of the available synapse models and/or is it possible to define your own? Kind regards, … [Next page](https://community.brain-map.org/tag/software/69.md?match_all_tags=true&page=1&tags%5B%5D=software)