# \#bug-report **URL:** https://community.brain-map.org/tag/bug-report/44.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:** 9\ **Last updated:** [June 28, 2026, 3:39am UTC](https://community.brain-map.org/t/brian-explorer-2/4855 "2026-06-28T03:39:08Z")
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… --- ## [Spinal atlas: images unavailable](https://community.brain-map.org/t/spinal-atlas-images-unavailable/4595)
**Author:** [@MarinM](https://community.brain-map.org/u/MarinM)\ **Replies:** 2\ **Last updated:** [July 31, 2025, 11:55am UTC](https://community.brain-map.org/t/spinal-atlas-images-unavailable/4595 "2025-07-31T11:55:02Z")
Images in the Allen Spinal Atlas have become unavailable. See for instance: Image Series :: Spinal Cord I have tried several genes, and none of the images are showing --- ## [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… --- ## [Gene expression matrix.cvs is too large to load it](https://community.brain-map.org/t/gene-expression-matrix-cvs-is-too-large-to-load-it/566)
**Author:** [@pommy](https://community.brain-map.org/u/pommy)\ **Replies:** 22\ **Last updated:** [October 8, 2024, 3:36pm UTC](https://community.brain-map.org/t/gene-expression-matrix-cvs-is-too-large-to-load-it/566 "2024-10-08T15:36:50Z")
I just download human/mouse brain matrix from https://portal.brain-map.org/atlases-and-data/rnaseq and found that these two matrix.csv files were too large to load it by read.csv(filepath,header=T,row.names=1). Is there… --- ## [Error in using allensdk module-session.stimulus\_presentations](https://community.brain-map.org/t/error-in-using-allensdk-module-session-stimulus-presentations/2029)
**Author:** [@mohamadamin-fjz](https://community.brain-map.org/u/mohamadamin-fjz)\ **Replies:** 2\ **Last updated:** [December 21, 2022, 8:02am UTC](https://community.brain-map.org/t/error-in-using-allensdk-module-session-stimulus-presentations/2029 "2022-12-21T08:02:19Z")
Hi everybody I m using allensdk to access brain observatory data. I try to load stimulus presentation data frame with session.stimulus\_presentations command but I get error:values should be boolean numpy array. Use the … --- ## [V1 & ALM - SMART-SEQ (2018) download links broken](https://community.brain-map.org/t/v1-alm-smart-seq-2018-download-links-broken/1142)
**Author:** [@krjenks](https://community.brain-map.org/u/krjenks)\ **Replies:** 1\ **Last updated:** [June 17, 2021, 8:30pm UTC](https://community.brain-map.org/t/v1-alm-smart-seq-2018-download-links-broken/1142 "2021-06-17T20:30:36Z")
Hello, thank you for providing all of these great single cell RNA-seq datasets and explorers. I wanted to take a closer look at the V1 & ALM - SMART-SEQ (2018) data for V1, but the download links appear to be broken. I… --- ## [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 … --- ## [Brain Explorer 2 crashes frequently on Mac/Catalina](https://community.brain-map.org/t/brain-explorer-2-crashes-frequently-on-mac-catalina/737)
**Author:** [@Arie](https://community.brain-map.org/u/Arie)\ **Replies:** 5\ **Last updated:** [March 14, 2021, 7:47pm UTC](https://community.brain-map.org/t/brain-explorer-2-crashes-frequently-on-mac-catalina/737 "2021-03-14T19:47:48Z")
I’ve run BE2 (human brain atlas) for the first time on macOS Catalina 10.15.7 (latest version). It displays no data when one selects any of the available structure. Multiple selections cause an immediate crash. For exa… --- ## [Mouse Spinal Cord Atlas high res single image viewer broke - Flash](https://community.brain-map.org/t/mouse-spinal-cord-atlas-high-res-single-image-viewer-broke-flash/922)
**Author:** [@Ralph](https://community.brain-map.org/u/Ralph)\ **Replies:** 1\ **Last updated:** [January 31, 2021, 3:25am UTC](https://community.brain-map.org/t/mouse-spinal-cord-atlas-high-res-single-image-viewer-broke-flash/922 "2021-01-31T03:25:22Z")
The Mouse Spinal Cord Atlas most important tool for viewing high res and downloading images, the single image viewer, is down. Example: ©2021 Allen Institute for Brain Science This alert appears: Your Adobe Flash Playe… --- ## [Conda Install BMTK](https://community.brain-map.org/t/conda-install-bmtk/862)
**Author:** [@Jonasver](https://community.brain-map.org/u/Jonasver)\ **Replies:** 3\ **Last updated:** [January 29, 2021, 11:35am UTC](https://community.brain-map.org/t/conda-install-bmtk/862 "2021-01-29T11:35:19Z")
Hi all, I recently installed BMTK through $ conda install -c kaeldai bmtk but am experiencing problems with the running the examples. For instance, when trying to run the EI-network, it is unable to open bmtk.builder.a… --- ## [Adobe flash player support ending?](https://community.brain-map.org/t/adobe-flash-player-support-ending/892)
**Author:** [@obaytas](https://community.brain-map.org/u/obaytas)\ **Replies:** 0\ **Last updated:** [January 13, 2021, 8:25pm UTC](https://community.brain-map.org/t/adobe-flash-player-support-ending/892 "2021-01-13T20:25:42Z")
So adobe flash player is no longer supported; end of life date was Dec31, 2020. Is there any action on this? thanks! --- ## [M1 10X Reference does not map to GRCh38.p2](https://community.brain-map.org/t/m1-10x-reference-does-not-map-to-grch38-p2/811)
**Author:** [@danielcgingerich](https://community.brain-map.org/u/danielcgingerich)\ **Replies:** 4\ **Last updated:** [December 18, 2020, 6:47pm UTC](https://community.brain-map.org/t/m1-10x-reference-does-not-map-to-grch38-p2/811 "2020-12-18T18:47:56Z")
I need to align the Human M1 10X dataset to GRCh38.p13 (ensembl v98). I can do this using ENSG IDs. However, the dataset on your website has no ENSG IDs. The corresponding publication states that the M1 dataset is from… --- ## [Mouse connectivity site down?](https://community.brain-map.org/t/mouse-connectivity-site-down/692)
**Author:** [@sebneuro](https://community.brain-map.org/u/sebneuro)\ **Replies:** 11\ **Last updated:** [December 11, 2020, 4:19pm UTC](https://community.brain-map.org/t/mouse-connectivity-site-down/692 "2020-12-11T16:19:14Z")
Hi, I’m having problems accessing the mouse connectivity data. I tried different computers and different browsers. Any idea if anything wrong with the database? --- ## [Mouse connectivity atlas down?](https://community.brain-map.org/t/mouse-connectivity-atlas-down/814)
**Author:** [@Annast](https://community.brain-map.org/u/Annast)\ **Replies:** 2\ **Last updated:** [December 11, 2020, 4:18pm UTC](https://community.brain-map.org/t/mouse-connectivity-atlas-down/814 "2020-12-11T16:18:47Z")
I experience problems when browsing for structures in the mouse brain connectivity atlas. The website works but it never returns the search results. It lasts for me for several days now. I have updates firefix but did no… --- ## [Slow download on NWB files from brain observatory Neuropixels data](https://community.brain-map.org/t/slow-download-on-nwb-files-from-brain-observatory-neuropixels-data/801)
**Author:** [@kinshuk](https://community.brain-map.org/u/kinshuk)\ **Replies:** 3\ **Last updated:** [December 8, 2020, 3:25am UTC](https://community.brain-map.org/t/slow-download-on-nwb-files-from-brain-observatory-neuropixels-data/801 "2020-12-08T03:25:39Z")
I’m trying to download the session data for the virual coding experiments using allensdk, but getting really slow download speeds (regardless of internet connection). Here’s the code I’m using: from allensdk.brain\_obse… --- ## [API overloaded by requests?](https://community.brain-map.org/t/api-overloaded-by-requests/809)
**Author:** [@MrBurnst](https://community.brain-map.org/u/MrBurnst)\ **Replies:** 1\ **Last updated:** [December 3, 2020, 8:30pm UTC](https://community.brain-map.org/t/api-overloaded-by-requests/809 "2020-12-03T20:30:48Z")
I’m getting This website is under heavy load We’re sorry, too many people are accessing this website at the same time. We’re working on this problem. Please try again later. whenever I want to query the API (http://a… --- ## [Ipfx 1.0.1 Release - Notice for Involved](https://community.brain-map.org/t/ipfx-1-0-1-release-notice-for-involved/700)
**Author:** [@isaak-willett](https://community.brain-map.org/u/isaak-willett)\ **Replies:** 0\ **Last updated:** [September 16, 2020, 10:42pm UTC](https://community.brain-map.org/t/ipfx-1-0-1-release-notice-for-involved/700 "2020-09-16T22:42:41Z")
Ipfx 1.0.1 was released on 9/16/2020 This release should not impact any projects. Bug fixes include: Decouples from AllenSDK docker images and introduces a dedicated image build for Ipfx This should not impact any u… --- ## [Downloading transcrip.tome file from mouse cortex+hippocampus dataset](https://community.brain-map.org/t/downloading-transcrip-tome-file-from-mouse-cortex-hippocampus-dataset/618)
**Author:** [@Sang.Seo](https://community.brain-map.org/u/Sang.Seo)\ **Replies:** 1\ **Last updated:** [July 24, 2020, 5:41pm UTC](https://community.brain-map.org/t/downloading-transcrip-tome-file-from-mouse-cortex-hippocampus-dataset/618 "2020-07-24T17:41:28Z")
Hi, I was hoping to download the transcrip.tome file for the mouse cortex+hippocampus dataset to have a play with it. I am unsure where I can obtain the HDF5 file from though. in the download section there were a bunch … --- ## [Brain Explorer 2 crashing when visualizing human gene data](https://community.brain-map.org/t/brain-explorer-2-crashing-when-visualizing-human-gene-data/208)
**Author:** [@PK\_Tan](https://community.brain-map.org/u/PK_Tan)\ **Replies:** 6\ **Last updated:** [May 27, 2020, 4:20am UTC](https://community.brain-map.org/t/brain-explorer-2-crashing-when-visualizing-human-gene-data/208 "2020-05-27T04:20:33Z")
Hi Community, I have been trying to visualize human brain gene expression data in the Brain Explorer 2 desktop software (Mac). I launch the explorer from the human microarray page for a particular gene (e.g. GRB14, see … --- ## [AllenSDK 0.16.3 released](https://community.brain-map.org/t/allensdk-0-16-3-released/188)
**Author:** [@nileg](https://community.brain-map.org/u/nileg)\ **Replies:** 0\ **Last updated:** [May 24, 2019, 12:47am UTC](https://community.brain-map.org/t/allensdk-0-16-3-released/188 "2019-05-24T00:47:29Z")
See the release notes here for details: ttps://github.com/AllenInstitute/AllenSDK/releases/tag/v0.16.3 This release fixes bugs in the example notebooks and removes AllenSDK’s dependence on scipy.misc.imresize.