Wojciech Krauze

Active limited-angle tomographic phase microscope.

Abstract. We demonstrate an active, holographic tomography system, working with limited angle of projections, realized by optical-only, diffraction-based beam steering. The system created for this purpose is a Mach–Zehnder interferometer modified to serve as a digital holographic microscope with a high numerical aperture illumination module and a spatial light modulator (SLM). Such a solution is fast and robust. Apart from providing an elegant solution to viewing angle shifting, it also adds new capabilities of the holographic microscope system. SLM, being an active optical element, allows wavefront correction in order to improve measurement accuracy. Integrated phase data captured with different illumination scenarios within a highly limited angular range are processed by a new tomographic reconstruction algorithm based on the compressed sensing technique: total variation minimization, which is applied here to reconstruct nonpiecewise constant samples. Finally, the accuracy of full measurement and the proposed processing path is tested for a calibrated three-dimensional micro-object as well as a biological object—C2C12 myoblast cell.

Generalized total variation iterative constraint strategy in limited angle optical diffraction tomography

Due to incompleteness of input data inherent to Limited Angle Tomography (LAT), specific additional constraints are usually employed to suppress image artifacts. In this work we demonstrate a new two-stage regularization strategy, named Generalized Total Variation Iterative Constraint (GTVIC), dedicated to semi-piecewise-constant objects. It has been successfully applied as a supplementary module for two different reconstruction algorithms: an X-ray type solver and a diffraction-wise solver. Numerical tests performed on a detailed phantom of a biological cell under conical illumination pattern show significant reduction of axial blurring in the reconstructed refractive index distribution after GTVIC is added. Analogous results were obtained with experimental data.

Problems and Solutions in 3-D Analysis of Phase Biological Objects by Optical Diffraction Tomography

Optical Diffraction Tomography is a technique for retrieving a 3-dimensional refractive index distribution from phase objects without destroying the structure of the samples. In the article we discuss the selection and implementation of full and limited angle version of tomographic reconstruction processes together with the analysis of different methods for gathering projections. We present two efficient implementations of full and limited angle tomographic systems including total processing paths and providing the examplary results of 3-D refractive index determination measurements of biological samples.

Limited-angle holographic tomography with optically controlled projection generation

In the paper we demonstrate a holographic tomography system with limited angle of projections, realized by optical– only, diffraction-based beam steering. The system created for this purpose is a Mach-Zehnder interferometer modified to serve as a digital holographic microscope with high Numerical Aperture illumination module and a Spatial Light Modulator. Such solution is fast and robust. Apart from providing an elegant solution to the viewing angle shifting, it also adds new capabilities of the holographic microscope system. SLM, being an active optical element, allows wavefront correction in order to improve measurement accuracy. Integrated phase data captured with different scenarios within a highly limited angular range are processed by a new tomographic reconstruction algorithm based on the compressed sensing technique: total variation minimization, which is applied to non-piecewise constant samples. Finally, the accuracy of full measurement and processing path proposed is tested for a calibrated 3D microobject.

Novel Perspectives on the Characterization of Species-Dependent Optical Signatures of Bacterial Colonies by Digital Holography

The use of light diffraction for the microbiological diagnosis of bacterial colonies was a significant breakthrough with widespread implications for the food industry and clinical practice. We previously confirmed that optical sensors for bacterial colony light diffraction can be used for bacterial identification. This paper is focused on the novel perspectives of this method based on digital in-line holography (DIH), which is able to reconstruct the amplitude and phase properties of examined objects, as well as the amplitude and phase patterns of the optical field scattered/diffracted by the bacterial colony in any chosen observation plane behind the object from single digital hologram. Analysis of the amplitude and phase patterns inside a colony revealed its unique optical properties, which are associated with the internal structure and geometry of the bacterial colony. Moreover, on a computational level, it is possible to select the desired scattered/diffracted pattern within the entire observation volume that exhibits the largest amount of unique, differentiating bacterial features. These properties distinguish this method from the already proposed sensing techniques based on light diffraction/scattering of bacterial colonies. The reconstructed diffraction patterns have a similar spatial distribution as the recorded Fresnel patterns, previously applied for bacterial identification with over 98% accuracy, but they are characterized by both intensity and phase distributions. Our results using digital holography provide new optical discriminators of bacterial species revealed in one single step in form of new optical signatures of bacterial colonies: digital holograms, reconstructed amplitude and phase patterns, as well as diffraction patterns from all observation space, which exhibit species-dependent features. To the best of our knowledge, this is the first report on bacterial colony analysis via digital holography and our study represents an innovative approach to the subject.

Limited-angle hybrid optical diffraction tomography system with total-variation-minimization-based reconstruction

Abstract. The case of diffraction tomography with limited angle of projections is discussed from the algorithmic and experimental points of view. To reconstruct a three-dimensional distribution of refractive index of a micro-object under study, we use a hybrid approach based on the simultaneous algebraic reconstruction technique (SART) enhanced by a compressed sensing reconstruction technique. It enables us to apply the standard computed tomography algorithms (which assume that the rays are traveling in straight lines through the object) for phase data obtained by means of digital holography. We present the results of analysis of a phantom and real objects obtained by applying SART with anisotropic total variation (ATV) minimization. The real data are acquired from an experimental setup based on a Mach–Zehnder interferometer configuration. Also, it is proven that in the case of simulated data, the limited number of projections captured in a limited angular range can be compensated by a higher number of iterations of the algorithm. We also show that the SART + ATV method applied for experimental data gives better results than the data replenishment algorithm.

Limited-angle hybrid diffraction tomography for biological samples

In the paper the case of diffraction tomography with limited angle of projections is discussed from the experimental and algorithmic point of views. To reconstruct a 3D distribution of refractive index of an object under study, we use the hybrid approach, which enables to apply the standard Computer Tomography algorithms for phase data obtained by digital holography. We present the results of applying Simultaneous Algebraic Reconstruction Technique together with Anisotropic Total Variation minimization (SART+ATV) on both a phantom object and real data acquired from an experimental setup based on a Mach-Zehnder interferometer configuration. Also, the analysis of the influence of the limited number of projections within a limited angular range is presented. We prove that in the case of simulated data, the limited number of projections captured in a limited angular range can be compensated by higher number of iterations of the algorithm. We also show that SART+ATV method applied for experimental data gives better results than the popular Data Replenishment algorithm.

Total variation iterative constraint algorithm for limited-angle tomographic reconstruction of non-piecewise-constant structures

Standard tomographic algorithms applied to optical limited-angle tomography result in the reconstructions that have highly anisotropic resolution and thus special algorithms are developed. State of the art approaches utilize the Total Variation (TV) minimization technique. These methods give very good results but are applicable to piecewise constant structures only. In this paper, we propose a novel algorithm for 3D limited-angle tomography – Total Variation Iterative Constraint method (TVIC) which enhances the applicability of the TV regularization to non-piecewise constant samples, like biological cells. This approach consists of two parts. First, the TV minimization is used as a strong regularizer to create a sharp-edged image converted to a 3D binary mask which is then iteratively applied in the tomographic reconstruction as a constraint in the object domain. In the present work we test the method on a synthetic object designed to mimic basic structures of a living cell. For simplicity, the test reconstructions were performed within the straight-line propagation model (SIRT3D solver from the ASTRA Tomography Toolbox), but the strategy is general enough to supplement any algorithm for tomographic reconstruction that supports arbitrary geometries of plane-wave projection acquisition. This includes optical diffraction tomography solvers. The obtained reconstructions present resolution uniformity and general shape accuracy expected from the TV regularization based solvers, but keeping the smooth internal structures of the object at the same time. Comparison between three different patterns of object illumination arrangement show very small impact of the projection acquisition geometry on the image quality.

Focus-tunable lens in limited-angle holographic tomography

In this paper a new, hardware-based solution for extending the depth of field in holographic tomography is presented. The solution is based on a 4f system and an electric, focus-tunable lens, which provides fast, motion-free defocusing of the plane conjugate with the camera, which acquires holograms. The optimum parameters for the required axial scanning are provided for a specific model of a commercially available tunable lens. Then, the quality of the system equipped with the designed module is analyzed and the reconstruction of a standard object (microsphere) scanned by the 4f-based defocusing system is presented. Finally, the result of the increased depth of field in the measurement domain is demonstrated with a reconstruction of a mouse fibroblast cell.

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

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.