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While ALiX was primarily written to analyze experimental data, it has become increasingly useful to analyze simulated data as well.Simulations can sometime provide intuition on the effect of various parameters on the outcome of a measurement, and are in general easier to come about than a full-fledged theory of the same phenomenon.
Two related projects are currently on-going to complement analysis capabilities:
- a SMS Simulator
- a SPAD Simulator
The goal of the SMS Simulator is to provide an engine for the generation of time stamps coming from individual molecules labeled with fluorescent reporters. In its initial iteration, the engine simulates simple Brownian diffusion in a pseudo-periodic box through a 3-dimensional Gaussian excitation/detection volume. A single fluorophore is modeled, but multiple molecules can be simulated at once. The simulator will eventually support multiple fluorophores per molecule, complex photophysics for each fluorophore, various excitation schemes (alternated, pulsed, polarized) and detection schemes (non-polarizing or polarizing beam-splitter, misalignment, aberrations, etc) and single-molecule dynamics.
The goal of the SPAD Simulator is to process the photons generated by the SMS Simulator and simulate their interaction with a SPAD, using a simplified model of such a device, including dark counts, afterpulsing, deadtime and, in the future, avalanche timing jitter and other possible effects.
These two tools will output data in the Photon-HDF5 format, allowing any software to process it, including ALiX.
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