BAMS Tutorial

For up to date issues or problems with this database please see the wiki.
For more information, please visit the Brain Architecture Management System.

BAMS, The Brain Architecture Management System is a searchable atlas and structure hierarchy where a set of authoritative data resides on the partitioning of the brain.

Most annotations are based on various atlases created by Dr. Swanson and colleagues, but BAMS lists data from other atlases. Note, if the same structure appears several times as a result in NIF, this may be the reason. If the structure was labeled in 4 atlases then there will be four entries, one for each atlas.

To get started searching for a brain region of interest is best, here we are searching for the “cerebellar peduncles”. We will use the autocomplete feature since this lets us know that the term of interest is both spelled correctly and in the NIF vocabulary.

Here the term has been searched on and 66 results are returned from brain region databases. We will select BAMS (in red) and see the associated information.

Here is a blow-up of the results set:
Note that the type of structure, nomenclature and species are all variables that produce individual entries. There are several entries from the mouse, from various atlases.

Clicking on the second result, from 2007 Doug Mouse atlas, takes us to the page in BAMS that contains more information and links to the brain region in question. Each section of this page contains a different set of data and we encourage you to explore them individually.

Major subparts are listed as well as super-parts, in this case the brain and cerebellum are higher than the peduncles, while the subparts include the Superior, Middle and Inferior cerebellar peduncles.

Clicking the Details button will produce a result set, similar to the one in NIF.

Clicking on the Tree link will take the user to a pop up window with all of the brain regions according to Doug 07, giving the user an idea of the hierarchy of brain regions that this atlas provides.

For more information, please visit the Brain Architecture Management System.