MUFASA: A Continuous-Time Stochastic Framework for Realistic Fluorescence Microscopy Simulation Article Swipe

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Wessim Omezzine , Sébastien Schaub , Laure Blanc-Féraud , Luca Calatroni ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.21203/rs.3.rs-6991954/v1

We present MUFASA (Multi-Protocol Unified Fluorescence-based Advanced Simulation Algorithm), a physically grounded, continuous-time simulator for super-resolution fluorescence microscopy. By modeling fluorophore dynamics using continuous-time Markov chains, MUFASA’s simulation features yield realistic photon emission behavior across both Single Molecule Localization Microscopy (SMLM) and fluorescence fluctuation-based (FF-SRM) protocols—independently of frame duration and sampling. The framework supports both individual emitters and structure-level simulations, incorporating photophysical transitions, photobleaching, and camera properties. To quantitatively validate simulations with real data, we introduce a novel validation metric based on the 1-Wasserstein distance between simulated and experimental photon-count distributions. In addition to simulation, another functionality estimates key photophysical parameters (e.g., molar extinction coefficient) and to suggest optimal light-source power ranges from fluctuation data. An intuitive Python-based graphical interface enables real-time parameter tuning, visualization, and TIFF export. Designed for biologists, physicists, microscopists, and numerical imaging engineers, MUFASA offers a practical platform for microscopy experiment design, hypothesis testing and the generation of realistic training data for data-driven microscopy methods across modalities.

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Fluorescence Microscope

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Fluorescence microscope Microscopy Fluorescence Computer science Biological system Nanotechnology Materials science Optics Physics Biology

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Type: preprint
Language: en
Landing Page: https://doi.org/10.21203/rs.3.rs-6991954/v1
PDF: https://www.researchsquare.com/article/rs-6991954/latest.pdf
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DOI: https://doi.org/10.21203/rs.3.rs-6991954/v1

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Title: MUFASA: A Continuous-Time Stochastic Framework for Realistic Fluorescence Microscopy Simulation

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Type: preprint

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Language: en

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Publication year: 2025

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Publication date: 2025-08-19

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Authors: Wessim Omezzine, Sébastien Schaub, Laure Blanc-Féraud, Luca Calatroni

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Landing page: https://doi.org/10.21203/rs.3.rs-6991954/v1

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Concepts: Fluorescence microscope, Microscopy, Fluorescence, Computer science, Biological system, Nanotechnology, Materials science, Optics, Physics, Biology

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