Holographic tomography: hardware and software solutions for 3D quantitative biomedical imaging (Invited paper)

Abstract

In this paper, we demonstrate the current concepts in holographic tomography (HT) realized within limited angular range with illumination scanning. The presented solutions are based on the work performed at Warsaw University of Technology in Poland and put in context with the state of the art in HT. Along with the theoretical framework for HT, the optimum reconstruction process and data visualization are described in detail. The paper is concluded with the description of hardware configuration and the visualization of tomographic reconstruction, which is calculated using a provided processing path.

Refractive Index Changes of Cells and Cellular Compartments Upon Paraformaldehyde Fixation Acquired by Tomographic Phase Microscopy

“…The 3D refractive index distribution in cells was obtained by means of a limited‐angle holographic tomography (LAHT) approach, which is the one of the most popular version of optical diffraction tomography in biomedical applications (2, 14, 22). In LAHT, the projections required for the 3D RI reconstruction are captured as individual holographic images of a sample that had been illuminated from different angles by scanning object illuminating beam while the camera and the sample are stationary.…”

“…This, however, does not allow to avoid any mechanical perturbation of the measured biological object and it is difficult to implement for investigations of samples at a Petri dish or a sample slide. In many LAHT systems, the “missing cone” problem is attempted to be solved by using a software approach with the most popular Gerchberg–Papoulis (GP) method with various regularization schemes (22). The currently best algorithmic solution, which offers increased reconstruction quality with highly minimized LAHT artifacts, is the total variation iterative constraint method (TVIC) combined with GP algorithm (23).…”

Bacteria Single-Cell and Photosensitizer Interaction Revealed by Quantitative Phase Imaging

“…The variation of the local RI values is associated with the examined object morphology but also with local fluctuations of its density, dependent from the chemical composition. Digital holographic tomography is based on a limited-angle holographic tomography [ 22 , 26 , 29 , 30 , 31 ] approach, which is one of the most popular versions of optical diffraction tomography used in biomedical examination. Living cells are complex structures that contain numerous organelles with different refractive indices [ 25 , 32 ].…”

3D-printed biological cell phantom for testing 3D quantitative phase imaging systems

“…Tomographic reconstruction algorithm used in this work was based on direct implementation of the Fourier diffraction theorem in the Rytov approximation. LAHT data were further processed with the iterative Gerchberg-Papoulis approach 26 with additional spatial support provided by the 3D mask computed with the total variation iterative constraint method 61 .…”

“…The metrological and comparative stage is especially important in the case of the techniques that intrinsically exhibit anisotropic spatial resolution. One example is limited-angle holographic tomography (LAHT) 26,27 as compared to its version based on the object rotation with illumination scanning 28 , in which additional reconstruction artifacts appear. In contrast, in the case of other well-established 3D imaging techniques the importance of comprehensive and systematic approach to the calibration of the measurement system has already been recognized 29–32 .…”