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Tutorials

Longer worked examples. Each one builds a complete simulation and explains the choices along the way. Each is also a Jupyter notebook: open it in Google Colab to run it without installing anything, or download it. The figures on these pages are made by running the code shown.

  • Two-color imaging of a cell

    Realistic ground truth from OpenOrganelle, fluorophores and filter sets from FPbase, and every step of the photon budget plotted. Widefield, then confocal.

  • Using your own ground truth

    Simulate any 3D array of fluorophore counts, in widefield and confocal.

  • Point-scanning detectors

    PMT high voltage and clipping, photon counting with a HyD, and line averaging, on one confocal image.

More examples are in the examples/ folder of the repository.