biopto / ewald Goto Github PK

EWALD is an open-source software that implements 3 optical diffraction tomography reconstruction algorithms, all based on Fourier Diffraction Theorem (FDT): (1) DI (Direct Inversion), GP (Gerchberg-Papoulis algorithm) and GPSC (Gerchberg-Papoulis with total-variation-based object-support constraint). It is dedicated for investigation of biological and technical samples, like cells, bacterias, optical fibers etc.

EWALD is a flexible software that allows:

• reconstruction of data in transmission and reflection mode, or both
• reconstruction of data captured with single or multiple wavelengths
• reconstruction of data captured in "limited angle" configuration (angular scanning of the laser beam with stationary sample and camera)
• reconstruction of data captured with stationary laser beam and a camera, with rotating sample

Example of tomographic reconstructions can be found here.

Currently, only the Matlab version of the software is available. To get the code running:

1. Download the repository
2. Download an example measurement dataset: Sinogram_03_hacat_03.mat.
3. Run the RecGTVIC.m file in Matlab.

If you want to use the GPSC algorithm with advanced total-variation minimization you need to make these 2 additional steps before running RecGTVIC.m:

1. Download ASTRA Tomography Toolbox astra-toolbox/astra-toolbox: ASTRA Tomography Toolbox (github.com) and add it to Matlab path.
2. Download linear-operator toolbox Spot mpf/spot: A linear-operator toolbox for Matlab (github.com) and add it to Matlab path.

Note, that you need to have CUDA on your computer to run GPSC!

The code is shared under GPLv3 license. If you use this code, please cite one of the following papers, depending on your application:

• if you use DI or GP reconstruction methods in transmission, please cite:

[1] W. Krauze, P. Makowski, M. Kujawińska, and A. Kuś, “Generalized total variation iterative constraint strategy in limited angle optical diffraction tomography,” Opt. Express 24(5), 4924–4936 (2016).

• if you use GPSC in transmission, please cite:

[2] W. Krauze "Optical diffraction tomography with finite object support for the minimization of missing cone artifacts," Biomed. Opt. Express 11(4), 1919-1926 (2020).

• if you use multiwavelength modality, please cite:

[3] P. Ossowski et al. "Near-infrared, wavelength, and illumination scanning holographic tomography," Biomed. Opt. Express 13(11), 5971-5988 (2022).

• if you use the reflection mode, please cite:

[4] W. Krauze, P. Ossowski, M. Nowakowski, M. Szkulmowski, M. Kujawińska "Enhanced QPI functionality by combining OCT and ODT methods," Proc. SPIE 11653, 19-24 (2021).

Main contributors:

• Piotr L. Makowski (2014-2018)
• Paweł Ossowski (2020-2022)
• Wojciech Krauze (2016-now)

Other contributors:

• Michał Ziemczonok
• Piotr Stępień.

ASTRA Tomography Toolbox astra-toolbox/astra-toolbox: ASTRA Tomography Toolbox (github.com)

pyl1 3cHeLoN/pyl1 (github.com)