Examples#
These runnable examples demonstrate the core workflows of massphoto, organised from fundamental single-molecule analysis to diagnostics and pipeline customisation:
Core analysis (1-3): Contrast-to-mass calibration, mass distribution fitting, and event landing rate over time.
Diagnostics & quality control (4-6): Stage drift compensation, noise floor evaluation with averaging windows, and movie properties over time.
Pipeline & extensibility (7-9): Step-by-step walk-through, custom candidate detection, and reproducible analysis records with replay.
Benchmark Datasets & Best Practice Protocol
The sample data used across these examples originates from the benchmark mass photometry recordings archived on Zenodo (10.5281/zenodo.15800729), accompanying Kratochvíl et al., Nat. Protoc. (2025), doi:10.1038/s41596-025-01255-4.
When running these examples for the first time, required data files (~1 GB total) are downloaded automatically from Zenodo and cached locally. An active internet connection is required on the first run; if a download times out due to network issues, re-running the command will retry files that were not fully downloaded.
