# \#connectivity **URL:** https://community.brain-map.org/tag/connectivity/30.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) --- ## [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… --- ## [Mouse brain connectivity correlative search](https://community.brain-map.org/t/mouse-brain-connectivity-correlative-search/3564)
**Author:** [@jonahb](https://community.brain-map.org/u/jonahb)\ **Replies:** 1\ **Last updated:** [September 9, 2024, 6:10pm UTC](https://community.brain-map.org/t/mouse-brain-connectivity-correlative-search/3564 "2024-09-09T18:10:50Z")
How is the correlation value calculated for the correlative search tool? Is there any documentation on this? --- ## [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! --- ## [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… --- ## [Why the connectivity paths only have non-zeros density/intensity at the last few entries](https://community.brain-map.org/t/why-the-connectivity-paths-only-have-non-zeros-density-intensity-at-the-last-few-entries/1025)
**Author:** [@orio](https://community.brain-map.org/u/orio)\ **Replies:** 0\ **Last updated:** [April 6, 2021, 5:12pm UTC](https://community.brain-map.org/t/why-the-connectivity-paths-only-have-non-zeros-density-intensity-at-the-last-few-entries/1025 "2021-04-06T17:12:44Z")
I tried to extract the paths of mouse brain connectivity of the injection experiments. Taking one path lines\[60\]\['path'\] as an example, why only the third to last and second to last entries have non-zero values for densi… --- ## [Why the transgenic lines of the same experiment don't match?](https://community.brain-map.org/t/why-the-transgenic-lines-of-the-same-experiment-dont-match/1007)
**Author:** [@orio](https://community.brain-map.org/u/orio)\ **Replies:** 5\ **Last updated:** [March 26, 2021, 1:27am UTC](https://community.brain-map.org/t/why-the-transgenic-lines-of-the-same-experiment-dont-match/1007 "2021-03-26T01:27:35Z")
I am looking at the connectivity data of experiment 156394513. From the website, the transgenic line used in the experiment should be A930038C07Rik-Tg1-Cre. But when I run the below code, 27 different transgenic lines s… --- ## [Is the Connectivity lines Information directly measured, or computed from density information?](https://community.brain-map.org/t/is-the-connectivity-lines-information-directly-measured-or-computed-from-density-information/1006)
**Author:** [@orio](https://community.brain-map.org/u/orio)\ **Replies:** 2\ **Last updated:** [March 25, 2021, 9:57pm UTC](https://community.brain-map.org/t/is-the-connectivity-lines-information-directly-measured-or-computed-from-density-information/1006 "2021-03-25T21:57:34Z")
Are the lines Information directly measured, or computed from density information? For example, in the below code, we can download the lines information around the coordinate (4400, 3300, 5600). Are the lines directly m… --- ## [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… --- ## [A question on the computation of laminar termination patterns in the cortex (Harris et al., 2019)](https://community.brain-map.org/t/a-question-on-the-computation-of-laminar-termination-patterns-in-the-cortex-harris-et-al-2019/791)
**Author:** [@lguyot](https://community.brain-map.org/u/lguyot)\ **Replies:** 1\ **Last updated:** [November 23, 2020, 7:27am UTC](https://community.brain-map.org/t/a-question-on-the-computation-of-laminar-termination-patterns-in-the-cortex-harris-et-al-2019/791 "2020-11-23T07:27:39Z")
Dear all, I am reading the article “The hierarchical organization of thalamic and cortical connectivity” by Harris et al., 2019. I would like to know in detail which formula is used to compute what is referred to as a … --- ## [Mapping the Human Brain](https://community.brain-map.org/t/mapping-the-human-brain/325)
**Author:** [@MaroonGomes](https://community.brain-map.org/u/MaroonGomes)\ **Replies:** 1\ **Last updated:** [October 31, 2019, 4:01pm UTC](https://community.brain-map.org/t/mapping-the-human-brain/325 "2019-10-31T16:01:23Z")
I feel this area really doesn’t get enough attention. In my opinion, being able to essentially upload someone’s brain onto a computer and combining that data with brain machine interfaces will definitely become something… --- ## [Mouse Connectivity Models - From Voxel to Coordinates](https://community.brain-map.org/t/mouse-connectivity-models-from-voxel-to-coordinates/470)
**Author:** [@FedeClaudi](https://community.brain-map.org/u/FedeClaudi)\ **Replies:** 1\ **Last updated:** [March 5, 2020, 10:15pm UTC](https://community.brain-map.org/t/mouse-connectivity-models-from-voxel-to-coordinates/470 "2020-03-05T22:15:03Z")
Hello everyone, I’ve recently started using the code from this repository for some analysis of connectivity data (https://github.com/AllenInstitute/mouse\_connectivity\_models). What I am trying to do is to look at conne… --- ## [BrainModules an interactive viewing tool](https://community.brain-map.org/t/brainmodules-an-interactive-viewing-tool/365)
**Author:** [@riichirohira](https://community.brain-map.org/u/riichirohira)\ **Replies:** 0\ **Last updated:** [November 23, 2019, 12:26pm UTC](https://community.brain-map.org/t/brainmodules-an-interactive-viewing-tool/365 "2019-11-23T12:26:32Z")
We have made an interactive viewing tool using the Allen database. https://web.ece.ucsb.edu/~riichirohira/TopBM-2.06/index.html Spencer Smith introduced this tool on twitter: We thank people who made the Allen Mous… --- ## [Matlab tool to visualize input output strength of specific brain area](https://community.brain-map.org/t/matlab-tool-to-visualize-input-output-strength-of-specific-brain-area/257)
**Author:** [@robertooooo](https://community.brain-map.org/u/robertooooo)\ **Replies:** 1\ **Last updated:** [September 5, 2019, 2:51pm UTC](https://community.brain-map.org/t/matlab-tool-to-visualize-input-output-strength-of-specific-brain-area/257 "2019-09-05T14:51:40Z")
Hi, I want to share a tool I recently wrote to visualize input and output of a brain area of interest in Matlab. https://github.com/Robertooooooo/BRIO . Happy to receive feedback! Cheers