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BIOMEDICAL IMAGING GROUP (BIG)
Laboratoire d'imagerie biomédicale (LIB)
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Students Projects

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Generating of Point-Spread Function for Advanced Imaging Microscopy in Python

Master Semester Project
Master Diploma
Project: 00449

00449

In modern microscopy, digital processes are decisive in many tasks, such as improving images by 3D deconvolution, achieving super-resolution or creating the ground-truth dataset required for supervised deep learning systems. The cornerstone of computational microscopy lies on knowledge of the point spread function (PSF), which sums up the entire image acquisition process. Thanks to the physical laws of light propagation and the laws of optics, we can generate synthetic yet highly realistic PSFs.

Building on our expertise gained from our PSF ImageJ plugin, PSFGenerator/Java, our goal is to provide a more precise and flexible tool. This involves integrating new modalities and transitioning to Python/PyTorch, all while maintaining a user-friendly interface.

This project involves a comprehensive review of PSF models, from basic to precise formulations, the theoretical foundation are already established. The student’s main role is coding—implementing various PSF models and extending applications to confocal, multiphoton, and STED microscopy. Additional task include interface development in a new open-source software package, called napari.

Prerequisites for this project include proficiency in Python and a good understanding of the Fourier transform. This opportunity beckons a motivated student to contribute to shaping the next generation of the PSF generator for the new cutting-edge imaging microscopy.

References on Microscopy PSF
  • https://en.wikipedia.org/wiki/Point_spread_function
  • https://svi.nl/Point-Spread-Function-(PSF)
  • https://www.youtube.com/watch?v=Tkc_GOCjx7E
  • Supervisors
  • Jonathan Dong, jonathan.dong@epfl.ch
  • Vasiliki Stergiopoulou , vasiliki.stergiopoulou@epfl.ch
  • Yan Liu and Daniel Sage, daniel.sage@epfl.ch
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