A full implementation of the Hough circle transform has finally come to ImageJ as a plugin: https://imagej.net/Hough_Circle_Transform.
The Hough circle transform is a powerful algorithm that can find and measure circular objects, even when they are embedded in complex and/or noisy backgrounds.
The implementation of both the transform itself and the search through the 3D Hough space is multi-threaded. The plugin also can also support movies, where it will iteratively perform the transform on each frame in the movie.
Outputs for the plugin include the raw transform, maps of the found centroids, and the ability to output the measured parameters to a results table.
The plugin is a modified and debugged version of the Hough circle transform from Hemerson Pistori and Eduardo Rocha Costa: https://imagej.nih.gov/ij/plugins/hough-circles.html. The transform algorithm is an optimized version is based off of a previous implementations by Mark Schulze.
Since this is my first serious foray into coding a plugin, and the bug search space is too large for one person to fully explore (although I think I got most of them), any feedback would be greatly appreciated.