FPM app: an open-source MATLAB graphical application for fast, simple and intuitive Fourier ptychographic microscopy data reconstruction

Mikołaj Rogalski

supervisor: Michał Józwik

In modern day medicine there is a need for large space-bandwidth product (SBP) cells bioimaging, i.e., imaging with both: large field of view and high resolution. One of the several techniques that can provide this is the Fourier ptychographic microscopy (FPM), which combines the information from multiple microscope images, each one collected at different illumination angle, to improve the resolution of a single image. Moreover, FPM iterative algorithms allow also for restoring the measured object phase i.e., the information about how much the light was delayed when passing through the sample (crucial in transparent samples imaging). Furthermore, FPM hardware can be straightforwardly assembled – in its basic configuration it requires only to modify a classical brightfield microscope by replacing its illuminator with a LED array.

However, despite hardware simplicity, FPM suffers from complex software implementation and up to this day, there wasn’t released any open-source algorithm allowing for its usage for a non-expert user. To fill this gap, as a part of this work there was developed an open-source MATLAB GUI application called the FPM app that allow for simple and intuitive FPM reconstruction. Moreover, inside the FPM app there were introduced several own modifications into the FPM processing path, that made it to perform faster and to be more automatic and robust. Its performance was also tested on experimental and synthetic datasets to confirm reconstruction correctness.