A simulator for Single Molelecule Localization Microscopy data.
In examples/ you can find examples on how to use the simulator:
- generate_and_visualize: A notebook whene you simply generate a simulated experiment and visualize it
- segments_arrangements: A notebook where you generate different simulated experiments, arranging the segmnets in each in different configurations
- generate_scenarios: A python script that generates a dataset containing the 4 scenarios we use for assessing clustering algorithms
- visualize: A python script to visualize a simulated experiment
In src/ you can find the source code:
- simulation: contains the core functions involved in the simulation
- various: contains various utility functions
Function simulate() generates a simulated experiment starting from predefined segment paths (which can be obtained e.g. with getChr21DLs) and following the specified parameters.
The disposition of probe localizations and false localizaions is based on https://github.com/JeremyPike/RSMLM (Pike, J. A., Khan, A. O., Pallini, C., Thomas, S. G., Mund, M., Ries, J., ... & Styles, I. B. (2020). Topological data analysis quantifies biological nano-structure from single molecule localization microscopy. Bioinformatics, 36(5), 1614-1621.)