Visual stack alignment
A key feature of Map Tracker is the visual alignment across multiple stack in a map.
Uses fudiciary point along the dendritic backbone and then each spines connection point to get a relative distance. Missing spines in a spine run are ‘snapped’ into place using the position along the dendritic backbone where the missing spine ‘would be’.
Fitting a line and radius to a dendritic backbone
Once a sequence of control points along the dendritic backbone are specified we use the Simple Neurite Tracer plugin in Fiji to fit a centerline along the dendritic backbone between each control point. This centerline is then made of a number of points, each point has an estimate of the radius of the dendritic backbone
Note: This fit is only as good as your raw data. If you have low signal to noise the estimate of the dendritic radius will not be very good.
Connecting a spine to the radius of a dendritic backbone
Each spine is semi-automatically connected to the backbone radius by searching for the brightest path between the spine head (the point you clicked to create the spine) and the nearby dendritic radius line.
Connecting spines from one stack to the next
A spine is connected from one stack to the next (in a map) using the position and angle of each spine. Two spines are connected if they (i) are within a threshold distance of each other and (ii) are on the same side of the dendrite.
Each spine is classified by the intensity profileof its ‘spine line’, the line connecting the spine head to the dendritic radius. [EXPLAIN THIS]