matlab implementation slimfast.m  (MathWorks Inc)

Journal: STAR Protocols

Article Title: Two-parameter single-molecule analysis for measurement of chromatin mobility

doi: 10.1016/j.xpro.2020.100223

Figure Lengend Snippet: Data pipeline for single-molecule tracking with SLIMfast.m (A) Single-molecule imaging .tif stacks are used as inputs for SLIMfast.m. (B) Screenshots from SLIMfast.m indicating how to load several .tif stacks as a batch to detect molecules in each consecutive frame, as well as the parameters that can be modified by the user depending on the characteristic of the microsope in use (see Notes of the section for details). (C) Screenshot from SLIMfast.m indicating how to load the particle data from the precedent step, for the script to trace single molecule trajectories. An example of the overlay of all detected particles in a nucleus expressing FOXA1-HALO, over the course of 50 s is displayed. (D) Example of trajectories established by the tracking algorithm in a single nucleus over the course of 50 s. A part of the corresponding .csv files is displayed, as provided after conversion by Csv_converter.m. The consecutive columns indicate #1, iteration; #2, frame of detection of the trajectory first step; #3, time = frame × step duration(0.01 s); #4 and #5, x and y coordinates (μm).

Article Snippet: The tracking step here is using the MATLAB-based SLIMfast.m script , a modified version of MTT , both publicly available.

Techniques: Imaging, Modification, Expressing