Software Tools
Are you doing microscopy-based feature finding, particle tracking, or microrheology, or are you thinking about it? This is how we analyze large amounts of time-lapse images in our lab. We developed these algorithms in MATLAB and then in Python (open source!), and have since made them ready for sharing, which we do here. Easy-to-follow tutorials/instructions are packaged with the code. If you’d like to obtain any of these code packages, just fill out a request below with a smidge about your project.
| 2D feature finding, pre-tracking and particle tracking employing centroid-based fitting, suited for spherical particles larger than the diffraction limit of the imaging system used — written in MATLAB | |
| 3D centroid-based feature finding with sub-pixel resolution in all three space dimensions — MATLAB Reference: Y. Gao and M. L. Kilfoil (2009) Opt. Express 17:4685-4704 | |
| Microrheology – including one-point, two-point, and de-drifting algorithms — MATLAB Reference: V. Pelletier, N. Gal, P. Fournier, and M. L. Kilfoil, (2009) Phys. Rev. Lett. 102:188303 | |
2D feature finding, pre-tracking and particle tracking algorithms in Python  | |
| 3D feature-finding algorithms in Python | |