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The paper presents development and validation of an inverse method for the identification of thermal characteristics of a short single laser pulse which stroke in a metal sample. The inverse method was applied to find unknown power of the laser pulse, the dimensionless shape parameter of the super-Gaussian function which describes the beam spatial profile as well as beginning and end times of the exposition of the metal sample to the laser pulse. The proposed inverse algorithm was based on the Levenberg-Marquardt technique as well as on temporal and spatial distributions of temperature on the rear surface of the sample, i.e., the opposite to the irradiated one, measured using the experimental stand. The performed investigations showed that the problem was ill-posed but good accuracy was obtained. The low sensitivity of registered temperature to changes in both power and duration of the pulse affected the retrieving accuracy most significantly. Moreover, the dependence of solution of the inverse problem on the initial guess was observed. The accuracy was also affected by low temporal resolution (500 Hz, with the exposure time from 0.2 to 1 ms) of the IR camera. This resolution affected the temporal sampling of measured temperatures. Despite these problems, the method was able to retrieve unknown pulse parameters with 20-25% accuracy.

Three‐dimensional quantitative phase imaging is an emerging method, which provides the 3D distribution of the refractive index (RI) and the dry mass in live and fixed cells as well as in tissues. However, an insufficiently answered question is the influence of chemical cell fixation procedures on the results of RI reconstructions. Therefore, this work is devoted to systematic investigations on the RI in cellular organelles of live and fixed cells including nucleus, nucleolus, nucleoplasm, and cytoplasm. The research was carried out on four different cell lines using a common paraformaldehyde (PFA)‐based fixation protocol. The selected cell types represent the diversity of mammalian cells and therefore the results presented provide a picture of fixation caused RI changes in a broader context. A commercial Tomocube HT‐1S device was used for 3D RI acquisition. The changes in the RI values after the fixation process are detected in the reconstructed phase distributions and amount to the order of 10−3. The RI values decrease and the observed RI changes are found to be different between various cell lines; however, all of them show the most significant loss in the nucleolus. In conclusion, our study demonstrates the evident need for standardized preparation procedures in phase tomographic measurements. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry. [ABSTRACT FROM AUTHOR]

As the 3D quantitative phase imaging (QPI) methods mature, their further development calls for reliable tools and methods to characterize and compare their metrological parameters. We use refractive index engineering during two-photon laser photolithography to fabricate a life-scale phantom of a biological cell with internal structures that mimic optical and structural properties of mammalian cells. After verification with a number of reference techniques, the phantom is used to characterize the performance of a limited-angle holographic tomography microscope. [ABSTRACT FROM AUTHOR]

Many building structures, due to a complex geometry and non-linear material properties, are cumbersome to analyze with finite element method (FEM). A good example is a self-supporting arch-shaped steel sheets. Considering the uncommon geometry and material profile of an arch (due to plastic deformations, cross section of a trough, a goffer pattern), the local loss of stability can occur in unexpected regions. Therefore, the hybrid experimental-numerical methodology of analysis and optimization of arch structures have been proposed. The methodology is based on three steps of development and validation of a FEM with utilization of a digital image correlation (DIC) method. The experiments are performed by means of 3D DIC systems adopted sequentially for each measurement step conditions from small size sections, through few segment constructions up to full scale in situ objects. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

This paper describes in detail the processing path leading to successful phase images stitching in digital holographic microscope for the extension of the field of view. It applies FIJI Grid/Collection Stitching Plugin, which is a general tool for images stitching, non‐specific for phase images. The FIJI plugin is extensively supported by aberration and phase offset correction. Comparative analysis of different aberration correction methods and data processing strategies is presented, together with the critical analysis of their applicability. The proposed processing path provides good background for statistical phase analysis of cell cultures and digital phase pathology. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

A successful application of self-interference digital holographicmicroscopy in combination with a sample-rotation-based tomography module for three-dimensional (3-D) label-free quantitative live cell imaging with subcellular resolution is demonstrated. By means of implementation of a hollow optical fiber as the sample cuvette, the observation of living cells in different 3-D matrices is enabled. The fiber delivers a stable and accurate rotation of a cell or cell cluster, providing quantitative phase data for tomographic reconstruction of the 3-D refractive index distribution with an isotropic spatial resolution. We demonstrate that it is possible to clearly distinguish and quantitatively analyze several cells grouped in a "3-D cluster" as well as subcellular organelles like the nucleoli and local internal refractive index changes. [ABSTRACT FROM AUTHOR]

Quantitative Phase Imaging (QPI) provides unique means for the imaging of biological or technical microstructures, merging beneficial features identified with microscopy, interferometry, holography, and numerical computations. This roadmap article reviews several digital holography-based QPI approaches developed by prominent research groups. It also briefly discusses the present and future perspectives of 2D and 3D QPI research based on digital holographic microscopy, holographic tomography, and their applications. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Holographic tomography (HT) is a measurement technique that generates phase images, often containing high noise levels and irregularities. Due to the nature of phase retrieval algorithms within the HT data processing, the phase has to be unwrapped before tomographic reconstruction. Conventional algorithms lack noise robustness, reliability, speed, and possible automation. In order to address these problems, this work proposes a convolutional neural network based pipeline consisting of two steps: denoising and unwrapping. Both steps are carried out under the umbrella of a U-Net architecture; however, unwrapping is aided by introducing Attention Gates (AG) and Residual Blocks (RB) to the architecture. Through the experiments, the proposed pipeline makes possible the phase unwrapping of highly irregular, noisy, and complex experimental phase images captured in HT. This work proposes phase unwrapping carried out by segmentation with a U-Net network, that is aided by a pre-processing denoising step. It also discusses the implementation of the AGs and RBs in an ablation study. What is more, this is the first deep learning based solution that is trained solely on real images acquired with HT.

Yokukansan (YKS) is a traditional Japanese herbal medicine that is increasingly being studied for its effects on neurodegenerative diseases. In our study, we presented a novel methodology for a multimodal analysis of the effects of YKS on nerve cells. The measurements of 3D refractive index distribution and its changes performed by holographic tomography were supported with an investigation by Raman micro-spectroscopy and fluorescence microscopy to gather complementary morphological and chemical information about cells and YKS influence. It was shown that at the concentrations tested, YKS inhibits proliferation, possibly involving reactive oxygen species. Also substantial changes in the cell RI after few hours of YKS exposure were detected, followed by longer-term changes in cell lipid composition and chromatin state., Competing Interests: The authors declare that there are no conflicts of interest related to this article., (© 2023 Optica Publishing Group under the terms of the Optica Open Access Publishing Agreement.)

We present a holographic tomography technique in which the projections are acquired using both wavelength and illumination scanning in the near-infrared region. We show how to process the acquired data to obtain correct values of three-dimensional refractive index distributions in both single-wavelength and multi-wavelength data acquisition schemes and how to properly account for the dispersion of the sample. We perform numerical and experimental comparisons of different illumination scenarios to determine the most efficient measurement protocol. We show that the multi-wavelength protocol is advantageous in terms of signal-to-noise ratio and contrast-to-noise ratio over single-wavelength protocols, even for the same number of projections used for reconstructions. Finally, we show that this approach is suitable for providing high-quality refractive index distributions of relatively thick colon cancer samples., Competing Interests: The authors declare no conflicts of interest., (© 2022 Optica Publishing Group under the terms of the Optica Open Access Publishing Agreement.)

Tomographic quantitative phase imaging (QPI) lacks an absolute refractive index value baseline, which poses a problem when large dense objects extending over multiple fields of view are measured volume by volume and stitched together. Some of the measurements lack the natural baseline value that is provided by the mounting medium with a known refractive index. In this work, we discuss the problem of the refractive index (RI) baseline of individual reconstructed volumes that are deprived of access to mounting medium due to the extent of the object. The solution of this problem is provided by establishing the RI offsets based on the overlapping regions. We have proven that the process of finding the offset RI values may be justifiably reduced to the analogous procedure in the 2D baseline correction (2D-BC). Finally, we proposed the enhancement of the state-of-the-art 2D-BC procedure previously introduced in the context of 2D QPI. The processing is validated at the examples of a synthetic dataset and a liver organoid., Competing Interests: The authors declare that there are no conflicts of interest related to this article., (© 2022 Optica Publishing Group under the terms of the Optica Open Access Publishing Agreement.)

Low-level laser therapy (LLLT) is a therapeutic tool that uses the photobiochemical interaction between light and tissue. Its effectiveness is controversial due to a strong dependence on dosimetric parameters. In this work, we demonstrate that digital holographic microscopy is an effective label-free imaging technique to analyze the effects of LLLT on biological cells, and we propose the full methodology to create correct synthetic aperture phase maps for further extensive, highly accurate statistical analysis. The proposed methodology has been designed to provide a basis for many other biological experiments using quantitative phase imaging. We use SHSY-5Y and HaCaT cells irradiated with different doses of red light for the experiment. The analysis shows quantitative changes in cell dry mass density and the projected cell surface in response to different radiation doses.

Quantitative phase imaging of cell cultures and histopathological slides often requires measurements in large fields of view which is realized through the stitching of multiple high resolution phase maps. Due to the characteristic properties of phase images, careful preprocessing is crucial for maintaining the metrological value of the stitched phase image. In this work, we present various methods that address those properties. Our efforts are focused on increasing robustness to minimize error propagation in consecutive preprocessing steps., Competing Interests: The authors declare that there are no conflicts of interest related to this article., (© 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement.)

In this work we propose an open-top like common-path intrinsically achromatic optical diffraction tomography system. It operates as a total-shear interferometer and employs Ronchi-type amplitude diffraction grating, positioned in between the camera and the tube lens without an additional 4f system, generating three-beam interferograms with achromatic second harmonic. Such configuration makes the proposed system low cost, compact and immune to vibrations. We present the results of the measurements of 3D-printed cell phantom using laser diode (coherent) and superluminescent diode (partially coherent) light sources. Broadband light sources can be naturally employed without the need for any cumbersome compensation because of the intrinsic achromaticity of the interferometric recording (holograms generated by -1 st and +1 st conjugated diffraction orders are not affected by the illumination wavelength). The results show that the decreased coherence offers much reduced coherent noise and higher fidelity tomographic reconstruction especially when applied nonnegativity constraint regularization procedure., Competing Interests: The authors declare no conflicts of interest., (© 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement.)

Holographic tomography (HT) is an advanced label-free optical microscopic imaging method used for biological studies. HT uses digital holographic microscopy to record the complex amplitudes of a biological sample as digital holograms and then numerically reconstruct the sample's refractive index (RI) distribution in three dimensions. The RI values are a key parameter for label-free bio-examination, which correlate with metabolic activities and spatiotemporal distribution of biophysical parameters of cells and their internal organelles, tissues, and small-scale biological objects. This article provides insight on this rapidly growing HT field of research and its applications in biology. We present a review summary of the HT principle and highlight recent technical advancement in HT and its applications.

The paper presents two novel, space-domain reconstruction algorithms for holographic tomography utilizing scanning of illumination and a fixed detector that is highly suitable for imaging of living biomedical specimens. The first proposed algorithm is an adaptation of the filtered backpropagation to the scanning illumination tomography. Its space-domain implementation enables avoiding the error-prone interpolation in the Fourier domain, which is a significant problem of the state-of-the-art tomographic algorithm. The second proposed algorithm is a modified version of the former, which ensures the spatially invariant reconstruction accuracy. The utility of the proposed algorithms is demonstrated with numerical simulations and experimental measurement of a cancer cell.

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.

A new holographic data processing path for accurate quantitative tomographic reconstruction of 3D samples placed in a cylindrical capillary is proposed. The method considers strong unintentional focusing effects induced by the inner cylindrical boundary of the vessel: 1) introduction of cylindrical wave illumination of a sample, and 2) object wave deformation. The first issue is addressed by developing an arbitrary illumination tomographic reconstruction algorithm based on filtered backpropagation, while the second by a novel correction algorithm utilizing the optical rays analysis. Moreover, the processing path includes a novel holographic method for correction of spherical aberration related to refraction at a planar surface. Utility of the developed data processing path is proven with numerical simulations and experimental measurement of a specially prepared test sample.