README.md

Rods detection in noisy images

This is a collection of ImageJ/FIJI macros for detection of rods (straight line segments of approximately same length) in noisy images and movies. Developed mostly for in vitro microtubule gliding assays, but can be applied to anything else (rod-shaped bacteria, etc). Uses Template matching plugin by Qingzong Tseng.

In addition, contains Matlab scripts to link detections to tracks based on modified SimpleTracker code by Jean-Yves Tinevez and tools to find tracks with directional runs (based on this paper).

For description and manual refer to Wiki page.
Main topics:

• How to install and run rods detection (ImageJ macro)
• How to compose detection to tracks (Matlab)
• How does detection work?
• Rods enchancement filter

Alternatively, to detect and track rods in movies with high signal-to-noise ratio, you can use FIESTA package from Stephan Diez lab, based on this publication.

Developed in Cell Biology group of Utrecht University.

E-mail for any questions.