This repository provides a curated set of MATLAB scripts developed for quantitative analysis and visualization of single-molecule fluorescence data, with specific focus on GFP-based SiMPull and TIRF microscopy experiments. Together, these tools form a modular workflow that enables spot counting, trace inspection, signal classification, and adaptive noise filtration for single-molecule kinetics and bleaching analyses. Count_gfp_spots: Automates GFP spot counting from paired hel.pks and hel.log files. The script reads time-stamped image metadata, quantifies single-molecule GFP events per frame, computes elapsed recording times, and generates an Excel report containing descriptive statistics, quartile-based outlier detection, and the full dataset. This tool provides a standardized framework for quantifying molecular binding events and assessing experimental stability over time. view_traces_New:Offers an interactive trace visualization interface for .traces files. The viewer displays individual intensity trajectories, allowing users to manually determine GFP signal onset and background levels. The program supports optional cropping of the x- (time) and y- (intensity) axes for precise inspection of relevant intervals and can overlay multiple traces sequentially to compare photobleaching or rebinding behavior across molecules. distribution_CKFilt:Classifies fluorescence traces from .traces datasets into vesicle-only, GFP-only, and both categories based on user-defined intensity thresholds and excitation timing. Each classified trace undergoes adaptive Chung–Kennedy (CK) filtering, a multi-window smoothing algorithm that preserves photobleaching transitions while reducing stochastic noise. Filtered traces are saved alongside cropped and annotated PNG visualizations marking GFP start and background levels, facilitating downstream analysis of stepwise bleaching. Transient_dwell: enables interactive dwell-time measurement from single-molecule fluorescence traces stored in .dat format. The program allows to load a folder of trace files, specify an initial time point and background intensity for visualization, and manually select time intervals corresponding to transient binding or bleaching events. For each trace, the intensity over time is displayed and the user can mark multiple time intervals. The dwell times (in seconds) are automatically calculated from those intervals and saved to a cumulative output file (dwelltime.dat) withing the same directory. Collectively, these MATLAB scripts enable reproducible single-molecule fluorescence analysis, including primary spot quantification and trace-level inspection and automated noise filtration supporting robust and transparent data processing in quantitative biophysics and fluorescence kinetics research.