Glossary

appearance widget - A widget to control the appearance of items, such as color, constract, brightness etc. Can be opened by a click on the colored box for each item in the Viewer Items List

connection/connectivity - A relation between nodes (voxels or regions) of a network. A connectivity has a certain value that defines how “strong” the connection is. Can be structural, functional etc. (depends on what the network is about)

connectivity matrix - Synonym for network

connectivity profile - Summary of voxel-level connectivity data (query item) in a region-level bar chart

database - BrainTrawler’s database is a term used to describe all data that BrainTrawler handles on the server

edge weight - The connectivity “strength” of an edge/connection (the relation between to nodes of a network)

expression profile - Summary of voxel-level gene expression data in a region-level bar chart.

gene expression query - Returns a list of genes ordered by their specificity for a volume of interest (VOI)

gene expression specificity - To account for regional specificity (i.e. genes can be expressed in the whole brain, which makes them not specific for VOI), we compute the mean gene expression within the VOI (similar to the Expression Query) and normalize it to the rest of the brain by computing the z-score

item - Spatial neurobiological data. Can be for example an 3D image, a network etc. see Item Types

network - A network consists of nodes (voxels or regions) and edges (connections). On a region level, they can be rather small (up to ~500 nodes), but on a voxel level they can have ten thousands of nodes with billions of connections

network query - A query executed on a network. For example target or source connectivity queries

query - A request on data in BrainTrawler’s database

query toolbar - A toolbar (Network Query and Gene Expression Query) on top of the screen to start brush selections and execute queries (Section 4)

region - A brain region. Defines an 3D area (volume) in the brain (=a set of adjacent voxels)

region selection state - All brain regions that are selected in the Parcellation Browser will be used for other UI elements (e.g. the Viewer Items List, Render View, Profiles)

target/source queries - Returns the aggregated outgoing (target) or incoming (source) connectivity of all voxels of a volume of interest (VOI)

UI - User interface

VOI - Volume of interest. A set of voxels, defining an arbitrary region in the brain

voxel - A value on a regular grid in 3D space. Like a pixel in a 2D image

visual query - A visual query allows requests to BrainTrawler’s database that are based on selections of a volume of interest (VOI) directly in the Render View

workflow - A specific task that can be performed to explore the data. Each workflow is represented as a tab on top of the site

workspace list - List of all items that are currently loaded into BrainTrawler (see Section 3.1)