Hi Ashley,
to be honest I do not have at the moment a really good idea of how to determine the width. What I am doing here is simply to determine the border of this structure an calculate the closest distance from the inner trajectory to this border using Nearest
. The code (continuing from the above) should be self explaining:
trajectoryPoints = PixelValuePositions[img3, 1];
order = Last[FindShortestTour[trajectoryPoints]];
trajectoryLinePoints = trajectoryPoints[[Rest@order]];
pp = First[1 /. ComponentMeasurements[img2, "PerimeterPositions"]];
Manipulate[
Graphics[{Line[pp], Red, Line[trajectoryLinePoints], Blue,
Circle[trajectoryLinePoints[[n]],
EuclideanDistance[trajectoryLinePoints[[n]],
First@Nearest[pp, trajectoryLinePoints[[n]]]]]}], {n, 1,
Length[trajectoryLinePoints], 1}]
This gives (as a demo for this idea):

Hopefully this helps a bit, regards -- Henrik