SerialTrack MATLAB code package
SerialTrack: ScalE and Rotation Invariant Augmented Lagrangian Particle Tracking
This repository contains the Matlab m-files to run our SerialTrack particle tracking algorithm. This code package includes both 2D and 3D particle tracking scripts for full-field 2D and 3D displacement fields, respectively. More details can be found in our SerialTrack paper (https://www.sciencedirect.com/science/article/pii/S2352711022001224).
Important pages
- Download latest version v1.0!
- [Example data] (https://minds.wisconsin.edu/handle/1793/82901)
- Manual
- FAQ
- Questions/Issues
- Bug Fixes/history
- Cite
- Franck Lab
Install and execute SerialTrack
Code installation
To run SerialTrack, please download MATLAB version later than 2021a and install these code packages/toolboxes:
- Curve fitting toolbox
- Image processing toolbox
- Parallel computing toolbox
- Statistics and Machine Learning Toolbox
- Wavelets analysis toolbox
Input Image Requirements
- 2D image sequences (at least two frames)
- 3D volumetric images (at least two volumetric stacks)
Images should have segment-able and localizable particles: limited or no particle clusters, particles distinguishable from noise, roughly spherically/cylindrically symmetric, size (roughly) 3 px to 20 px diameter. See examples of particles in the test cases. Custom pre-processing, segmentation, and localization codes can be straightforwardly incorporated (and are encouraged for challenging imaging or specimen conditions).
Running included example case
- Make sure that the main files and the supplemental m files (from file exchange) are added to the path in Matlab.
- Download and save the [example data sets] in the "./imgFolder" folder.
- Run the example*.m files in the folder "./Example_main_files"
- Edit the paths for SerialTrack and images (as needed)
- Check for lines labeled "TODO" and follow instructions (as needed)
Cite
If used please cite: [1] Jin Yang, Yue Yin, Alexander K. Landauer, Selda Buyuktozturk, Jing Zhang, Luke Summey, Alexander McGhee, Matt K. Fu, John O. Dabiri, Christian Franck. SerialTrack: ScalE and Rotation Invariant Augmented Lagrangian Particle Tracking. SoftwareX, Volume 19, 101204 (2022) https://www.sciencedirect.com/science/article/pii/S2352711022001224
Contact and support
For questions, please first refer to FAQ and Questions/Issues. Add a new question if similar issue hasn't been reported. The author's contact information can be found at Franck Lab.