Reconstruction method for extended depth-of-field optical diffraction tomography

Abstract

In the paper we present a novel method of extended depth-of-field limited-angle optical diffraction tomography, in which the change of a focal plane position is performed with a liquid focus-tunable lens. One sinogram is acquired for each state of a focus-tunable lens. After acquisition process is complete, all sinograms are independently reconstructed and stitched to form the final tomographic reconstruction. The presented solution effectively extends the applicability of the Rytov approximation to relatively thick samples and provides uniform resolution of 3D tomographic reconstructions. The method is also combined with Generalized Total Variation Iterative Constraint algorithm, which minimizes distortion of the results due to the limited angular range of acquired projections. The combined solution is dedicated to investigation of transparent and semi-transparent biological micro-structures, like cells and tissue slices.

Large-scale high-sensitivity optical diffraction tomography of zebrafish

“…The time it takes to do a complete 3D reconstruction of a zebrafish is thus approximately 12 hours. Apart from using the four available cores in paralel to do the calculations, we did not optimize the reconstruction algorithm, but expect that significant improvements in computational speed are still possible, for example through using CUDA programming of the FBP reconstruction [26].…”

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

“…This leads to a highly limited DOF, which degrades the result. To further improve reconstruction quality, it is possible to extend the DOF in reconstruction either numerically or using a hardware approach . The computational enhancement based on numerical defocusing provides outstanding improvement .…”

“…The computational enhancement based on numerical defocusing provides outstanding improvement . However, the calculations are time‐consuming and the equivalent hardware solution may be obtained at additional measurement time instead . The hardware approach requires an additional module, as shown by the extension presented in Figure D, added to an HT system instead of a camera.…”

“…However, the results are visibly affected by the stairway artifacts characteristic for TV minimization, which tends to the obscure the finer details of typical microbiological samples. In the following section, we outline a different proposition of utilizing TV in LAODT , which can be based on any iterative algorithm with spatial support capability, including the basic GP scheme described above.…”

“…We discuss the inherent limitations of this approach from the perspectives of hardware and software with emphasis on the quality of depth reconstruction. Then, we review a few practical strategies to circumvent the limitations with minimal system complexity and cost, including the solutions developed by our group . Section briefly states the theoretical basis of LAODT with emphasis on the practical effects of involved approximations in the context of cytology.…”