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SMLM Simulator

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

Working scheme

Function simulate() generates a simulated experiment starting from predefined segment paths (which can be obtained e.g. with getChr21DLs) and following the specified parameters.

Credits:

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.)