# Neo-Cortex Anatomy Database for Neuroscience Community (A Crowd Sourcing Approach?)

**URL:** <https://discourse.numenta.org/t/neo-cortex-anatomy-database-for-neuroscience-community-a-crowd-sourcing-approach/8359>\
**Category:** General Neuroscience\
**Tags:** community\
**Created:** [March 27, 2021, 8:18am UTC](https://discourse.numenta.org/t/neo-cortex-anatomy-database-for-neuroscience-community-a-crowd-sourcing-approach/8359 "2021-03-27T08:18:51Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![adam](https://avatars.discourse-cdn.com/v4/letter/a/4af34b/32.png) [@adam](https://discourse.numenta.org/u/adam)\
**Post date:** [March 27, 2021, 8:18am UTC](https://discourse.numenta.org/t/neo-cortex-anatomy-database-for-neuroscience-community-a-crowd-sourcing-approach/8359/1 "2021-03-27T08:18:51Z")

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Hey everyone,

I have a question: does anybody know an **open database** , where information on the **anatomy** of the **neocortex** is collected?

Reason: I usually have troubles finding the right papers to do my research. It is usually very hard to find information to specific questions, e.g. you might want to check: what is the connection probability between the L5 thick tufted cells and L6 cortico-thalamic neurons? To which dendritic segments do they connect, how is this different across species, etc.  
I think a lot of this information is out there, but hidden deep in some papers and not easily accessible. For me the hardest part is to find those papers and extract what they have to say on specific connections. Usually you have to check multiple papers to get a better overview.

I think a database collection with this information and referencing the original material could be beneficial to many people, and some of them could be willing to extend it, similar to Wikipedia.  
However I do not know of such a project and wanted to ask if anybody does.

I can also see some troubles:

- how to structure it? Using tags like L5, L6a, thick-tufted, cortico-thalamic, etc.
- can this be integrated into existing projects, like Wikipedia?

Would be cool to hear your thoughts and doubts! And also how you usually do your research and how you test your hypothesis (to fit it to the data).

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**Author:** ![mraptor](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.numenta.org/mraptor/32/4469_2.png) [@mraptor](https://discourse.numenta.org/u/mraptor)\
**Post date:** [March 27, 2021, 4:13pm UTC](https://discourse.numenta.org/t/neo-cortex-anatomy-database-for-neuroscience-community-a-crowd-sourcing-approach/8359/2 "2021-03-27T16:13:01Z")

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may be Numenta can host a Wiki and seed it with their current understanding and give it the initial structure.

And we can help. (As a start transfer HTM Cheatsheet)

As addition anyone who tried to implement HTM and TBT can write expose and link to their project, which can help us a keep track and help Numenta measure the impact of the theory

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**Author:** ![Bitking](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.numenta.org/bitking/32/3099_2.png) [@Bitking](https://discourse.numenta.org/u/Bitking)\
**Post date:** [March 28, 2021, 12:08am UTC](https://discourse.numenta.org/t/neo-cortex-anatomy-database-for-neuroscience-community-a-crowd-sourcing-approach/8359/3 "2021-03-28T00:08:32Z")

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Have you seen this?

> [@Other HTM projects](https://discourse.numenta.org/t/other-htm-projects/2163):
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> SEE ALSO: [HTM Implementations](https://numenta.org/implementations/) Projects (with sources): Language/Runtime Project Link Description Last Activity (as at June 2019) Python [iHTM](https://github.com/vsraptor/ihtm)[docs!](https://github.com/vsraptor/ihtm/docs) March 2021 Python [bbHTM](https://github.com/vsraptor/bbhtm)[great docs!](https://github.com/vsraptor/bbhtm/docs) May 2016 [pyHTM](https://github.com/carver/pyHTM) April 2011 [cla](https://github.com/gilsho/cla) February 2013 javascript [nupic-js](https://github.com/iandanforth/nupic-js) May 2014 [htm.JavaScript](https://github.com/htm-community/htm.JavaScript) by Ralf Seliger June 2015 [HTM.js](https://github.com/htm-community/htm.js) This project by @Paul_Lamb is a test implementation of HTM created to help Paul learn the basics, explore new concepts and theories, and share demos. It is designed to…

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**Author:** ![dmac](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.numenta.org/dmac/32/5842_2.png) [@dmac](https://discourse.numenta.org/u/dmac)\
**Post date:** [March 28, 2021, 1:21am UTC](https://discourse.numenta.org/t/neo-cortex-anatomy-database-for-neuroscience-community-a-crowd-sourcing-approach/8359/4 "2021-03-28T01:21:02Z")

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I think this is what you’re looking for: [Microcircuit - nmc-portal](https://bbp.epfl.ch/nmc-portal/microcircuit.html) and that data came from [Home - nmc-portal](https://bbp.epfl.ch/nmc-portal/welcome.html)

Both the Allen institute and the Blue Brain Project have publicly released a lot of data in easy to use formats. They have some nice GUI interfaces for exploring the data. It can take a bit of poking around to find all of their best work, but it is all linked to from their home pages:

- Allen institute: [https://portal.brain-map.org/](https://portal.brain-map.org/)
- BBP: [https://portal.bluebrain.epfl.ch/](https://portal.bluebrain.epfl.ch/)

* * *

When reading research papers, try to start with “Review” articles.  
Also, try to start with articles which were published in the past 10-20 years.  
“Alex M. Thomson” has written a number of good review articles about the cortex.

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**Author:** ![mraptor](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.numenta.org/mraptor/32/4469_2.png) [@mraptor](https://discourse.numenta.org/u/mraptor)\
**Post date:** [March 28, 2021, 3:16am UTC](https://discourse.numenta.org/t/neo-cortex-anatomy-database-for-neuroscience-community-a-crowd-sourcing-approach/8359/5 "2021-03-28T03:16:54Z")

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> [@Other HTM projects](https://discourse.numenta.org/t/other-htm-projects/2163/1):
>
> Python [bbHTM](https://github.com/vsraptor/bbhtm) [great docs!](http://ifni.co/bbHTM.html)

this is now here :

> **[GitHub - vsraptor/bbhtm: bare bone Hierarchial Temporal Memory](https://github.com/vsraptor/bbhtm)**
>
> bare bone Hierarchial Temporal Memory. Contribute to vsraptor/bbhtm development by creating an account on GitHub.

under docs…

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<div class="post-metadata">

**Author:** ![adam](https://avatars.discourse-cdn.com/v4/letter/a/4af34b/32.png) [@adam](https://discourse.numenta.org/u/adam)\
**Post date:** [March 29, 2021, 8:18am UTC](https://discourse.numenta.org/t/neo-cortex-anatomy-database-for-neuroscience-community-a-crowd-sourcing-approach/8359/6 "2021-03-29T08:18:45Z")

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thanks dmac for the links: I knew the [Microcircuit - nmc-portal](https://bbp.epfl.ch/nmc-portal/microcircuit.html), but I didnt look up the literature, but just used the tool to explore the data. Thanks for that pointers, I will dive deeper!

Maybe helpful to others: [http://www.mouselight.janelia.org/](http://www.mouselight.janelia.org/)

- you can query for specific neurons in almost all parts of the brain and then select some of them and visualize (3D!!) how they project.
- I found this pretty and amazing, that this is possible as well as how far individual neurons can project!

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**Author:** ![mraptor](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.numenta.org/mraptor/32/4469_2.png) [@mraptor](https://discourse.numenta.org/u/mraptor)\
**Post date:** [March 29, 2021, 4:07pm UTC](https://discourse.numenta.org/t/neo-cortex-anatomy-database-for-neuroscience-community-a-crowd-sourcing-approach/8359/7 "2021-03-29T16:07:07Z")

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All those links seems to be for mouse brains … do we have connectivity for human brain