FPM is a computational microscopy technique that allows obtaining microscopic image of a measured sample with much higher resolution than it would follow from the numerical aperture (NA) of used microscope objective. Such high resolution is obtained by combining in the Fourier domain information about the measured specimen from different illumination directions. This advantage combined with the fact that low NA objectives are characterized by low magnification, allows obtaining a high-resolution image of a specimen with a large field of view. Moreover, iterative algorithms used in the process of reconstruction, enable obtaining information not only about the amplitude but also about the phase of the sample The phase distribution is especially significant in the case of bioimaging, as living cells are known to be semi-transparent objects with low amplitude, hence difficult to see under the classical brightfield microscope).
FPM app is first, to the best of our knowledge: simple, intuitive, universal, semi-automatic, open to modify, GUI open-source app that allows users to perform straightforward reconstruction of original FPM datasets, without requiring the user to have specialized knowledge in the field of imaging or programming. FPM app was created in MATLAB (based on Lei Tian algorithm - http://sites.bu.edu/tianlab/open-source/) and all MATLAB codes (that are free to modify for personal use) along with standalone executable version and full FPM app documentation can be found in https://github.com/MRogalski96/FPM-app/releases.
FPM app is released in 2 versions:
- MATLAB version - it contains a pack of MATLAB codes, which are used to open FPM app through MATLAB. These codes are open to be modified, to adjust FPM app to a given set of preferences or to further improve it.
- Executable version – it contains FPMAppInstaller_web.exe that installs FPMapp.exe along with all the necessary files and MATLAB Runtime that is required to run MATLAB standalone applications.
To FPM app is attached documentation that consists:
- Description of FPM app working overflow and all FPM app windows
- Methods used for processing the FPM data
- Description of our innovations into the FPM processing path
- A tips for modifying FPM app
- Exemplary description of collecting and reconstructing FPM data process
FPM app was developed by Mikolaj Rogalski as a part of master's thesis at Faculty of Mechatronics, Warsaw University of Technology, Warsaw, Poland
Mikołaj Rogalski, Piotr Zdańkowski, Maciej Trusiak, FPM app: an open-source MATLAB application for simple and intuitive Fourier ptychographic reconstruction, Bioinformatics, 2021;, btab237, https://doi.org/10.1093/bioinformatics/btab237
In case of any problem with FPM app please contact the author: [email protected]