# \#brain-explorer **URL:** https://community.brain-map.org/tag/brain-explorer/20.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… --- ## [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… --- ## [How to switch between the 3 coordinate systems of Mouse Connectivity?](https://community.brain-map.org/t/how-to-switch-between-the-3-coordinate-systems-of-mouse-connectivity/952)
**Author:** [@orio](https://community.brain-map.org/u/orio)\ **Replies:** 6\ **Last updated:** [September 26, 2022, 10:12pm UTC](https://community.brain-map.org/t/how-to-switch-between-the-3-coordinate-systems-of-mouse-connectivity/952 "2022-09-26T22:12:39Z")
There are 3 coordinate systems for mouse connectivity. The output of get\_projection\_density() of allensdk.core.mouse\_connectivity\_cache. It is (AP, DV, ML) and have the size of 528x320x456 (Unit: voxel). Bregma is roug… --- ## [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 … --- ## [How are the edges of the mouse connectivity data drawn in the Brain Explorer?](https://community.brain-map.org/t/how-are-the-edges-of-the-mouse-connectivity-data-drawn-in-the-brain-explorer/957)
**Author:** [@orio](https://community.brain-map.org/u/orio)\ **Replies:** 1\ **Last updated:** [February 24, 2021, 11:58pm UTC](https://community.brain-map.org/t/how-are-the-edges-of-the-mouse-connectivity-data-drawn-in-the-brain-explorer/957 "2021-02-24T23:58:17Z")
In the Brain Explorer there are nodes and edges in the mouse connectivity data. I think I’m able to obtain the nodes’ data in the SDK, but I’m not sure if the edges’ data is available in the SDK (see below image). For e… --- ## [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 … --- ## [Tutorials for Brain Explorer software](https://community.brain-map.org/t/tutorials-for-brain-explorer-software/157)
**Author:** [@kaitlync](https://community.brain-map.org/u/kaitlync)\ **Replies:** 1\ **Last updated:** [January 2, 2020, 5:06pm UTC](https://community.brain-map.org/t/tutorials-for-brain-explorer-software/157 "2020-01-02T17:06:22Z")
The Allen Brain Explorer application is a great tool to explore brain anatomy and access data in the Allen Mouse Brain Atlas, Allen Mouse Brain Connectivity Atlas, and reference atlas for the mouse brain. Information on … --- ## [Access connectivity streamline data](https://community.brain-map.org/t/access-connectivity-streamline-data/144)
**Author:** [@erpuntbakker](https://community.brain-map.org/u/erpuntbakker)\ **Replies:** 23\ **Last updated:** [October 16, 2019, 4:34pm UTC](https://community.brain-map.org/t/access-connectivity-streamline-data/144 "2019-10-16T16:34:15Z")
The new and beautiful web-based Brain Explorer shows streamlines when selecting a mouse connectivity experiment. The raw microscopic sections have been available for quite some time, but I can’t get my hands on the proce… --- ## [Allen Brain Explorer functionality: Loading 3D Brain Reference Map Models into MatLab/Python/R](https://community.brain-map.org/t/allen-brain-explorer-functionality-loading-3d-brain-reference-map-models-into-matlab-python-r/212)
**Author:** [@Brandon](https://community.brain-map.org/u/Brandon)\ **Replies:** 2\ **Last updated:** [September 23, 2019, 3:23pm UTC](https://community.brain-map.org/t/allen-brain-explorer-functionality-loading-3d-brain-reference-map-models-into-matlab-python-r/212 "2019-09-23T15:23:50Z")
We have been asked the following questions from the community: Q: Is there a way to save an image from the Allen Brain Explorer beta? Is it possible to open the 3D image of structures and projections of choice in Matla… --- ## [View my own volumetric data in BrainExplorer](https://community.brain-map.org/t/view-my-own-volumetric-data-in-brainexplorer/247)
**Author:** [@jw156605](https://community.brain-map.org/u/jw156605)\ **Replies:** 1\ **Last updated:** [August 22, 2019, 3:44pm UTC](https://community.brain-map.org/t/view-my-own-volumetric-data-in-brainexplorer/247 "2019-08-22T15:44:54Z")
Is it possible to load my own volumetric data into the brain explorer? For example, suppose I wanted to take the cell coordinates from this study (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280067/) and view them alon… --- ## [Help saving data on brain explorer](https://community.brain-map.org/t/help-saving-data-on-brain-explorer/178)
**Author:** [@Sarah](https://community.brain-map.org/u/Sarah)\ **Replies:** 1\ **Last updated:** [May 23, 2019, 4:54pm UTC](https://community.brain-map.org/t/help-saving-data-on-brain-explorer/178 "2019-05-23T16:54:36Z")
Hello, I have been trying to save data on brain explorer but it does not allow me to. Under file, the save data set does not work for me. Is there anything I can do about it? Thank you for helping --- ## [Mouse brain volume](https://community.brain-map.org/t/mouse-brain-volume/105)
**Author:** [@bendichter](https://community.brain-map.org/u/bendichter)\ **Replies:** 3\ **Last updated:** [February 26, 2019, 2:03am UTC](https://community.brain-map.org/t/mouse-brain-volume/105 "2019-02-26T02:03:17Z")
Is there a 3D mouse brain volume available? How would I access this data?