Supplemental Material: Analysis of quasi-stationary multiple binding sites
Niewidok et al. "Single-Molecule Imaging Reveals Dynamic Biphasic Partition of RNA-Binding Proteins in Stress Granules"
Procedure:
- Smooth image by spatial median (https://de.mathworks.com/matlabcentral/fileexchange/25825-hybrid-median-filtering?focused=5147556&tab=function) and subsequent temporal median
- Localize molecules by MTT algorithm (https://www.nature.com/articles/nmeth.1233)
- Extract transient immobilization event by DBSCAN principle with smDBSCAN.m
- Link immobilization events
- Extract x-t and y-t-kymographs
- Decompose kymographs into binding sites by STASI algorithm (http://pubs.acs.org/doi/abs/10.1021/jz501435p)
- Calculate pair-wise distances between binding sites
Source Code:
smDBSCAN.m: applies the DBSCAN principle of density-reachability to group subsequent observations of the same immobile single-molecule over time.
DBSCAN_fwd_rev_cluster.m: performs pure forward and reverse-looking clustering using the DBSCAN principle followed by fusion via maximum core point overlap
DBSCAN_pot_link.m: finds points that potentially belong into one group
DBSCAN_hard_thresh.m: reduces the list of potential links to those that reside within the expected time window around each point
DBSCAN_point_score.m: calculates the density score for each point
DBSCAN_group.m: implements point clustering based on the principle of DBSCAN (Density-Based Spatial Clustering of Applications with Noise). DBSCAN is a data clustering algorithm proposed by Martin Ester, Hans-Peter Kriegel, Jörg Sander and Xiaowei Xu in 1996.
show_me_my_cluster.m: visualizes the results of the clustering process