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

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).


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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Have you seen this?

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I think this is what you’re looking for: Microcircuit - nmc-portal and that data came from Home - nmc-portal

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:

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.


this is now here :

under docs…

thanks dmac for the links: I knew the Microcircuit - nmc-portal , 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:

  • 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!

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