BAMS Connections 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 brain connectivity in addition to brain parts and cell types.

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 V1.

Under the Data Federation tab, 6108 results came up for the V1 search and these include the connectivity data. This data can be found under the Data Type: Connectivity tab.

The output region is the origin of the connection and the target region represents the target, while the projection strength can “exist” or have a qualitative value like “strong” or “weak”. The species and reference atlas are referenced under the nomenclature column and additional information is visible in the reference column. There are no links out in to this resource as the data presented here in a table are presented in a graphical way in BAMS so we encourage you to search there for additional data. Through the BAMS interface one can specify target and output regions as well as projection strengths. The NIF data do not include “no projection” data, but BAMS maintains this data and one can query their system for it.

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