Auto connect. Automatically connect a spine to the backbone radius. Stack, Map Stack, Algorithms.
Backbone. The centerline of a filament like structure. Examples of filament like structures are dendrites and axons.
Backbone radius. Each point along a backbone has a radius. The set of radius points makes a backbone radius line. When spines are connected to a dendrite, they are connected to this backbone radius. For axons, boutons are connected to the backbone itself (assuming axonal radius is hard to estimate).
Connection Distance. Each spine is connected to a point on the radius line along a backbone. The backbone line has a distance defined as 0 at the fiduciary point, increasing in one direction and decreasing in the other. Direction (positive and negative distances along the backbone line) is determined by the order the backbone was created using control points (see making a map).
Fiduciary Point. A point along the backbone defined as 0 distance. MAp MAker used fiduciary points across multiple stacks to automatically connect (with errors) spines. Two spines are connected if they fall within a threshold distance along the backbone. See: Options.
Fiji: Fiji Is Just Image J. A distribution of ImageJ that is designed to make life easier for biologists by including a large number of plugins with a clear organization.