Hybrid Iterating-Averaging Low Photon Budget Gabor Holographic Microscopy.

It is well known that the quantitative phase information which is vital in the biomedical study is hard to be directly obtained with bright-field microscopy under incoherent illumination. In addition, it is impossible to maintain the living sample in focus over long-term observation. Therefore, both the autofocusing and quantitative phase imaging techniques have to be solved in microscopy simultaneously. Here, we propose a lightweight deep learning-based framework, which is constructed by residual structure and is constrained by a novel loss function model, to realize both autofocusing and quantitative phase imaging. It outputs the corresponding in-focus amplitude and phase information at high speed (10fps) from a single-shot out-of-focus bright-field image. The training data were captured with a designed system under a hybrid incoherent and coherent illumination system. The experimental results verify that the focused and quantitative phase images of non-biological samples and biological samples can be reconstructed by using the framework. It provides a versatile quantitative technique for continuous monitoring of living cells in long-term and label-free imaging by using a traditional incoherent illumination microscopy system.

Hybrid Random Walk-Linear Discriminant Analysis Method for Unwrapping Quantitative Phase Images of Biological Samples

Inflammatory bowel diseases (IBD) are inflammatory disorders of the gastrointestinal tract characterized by a chronic relapsing disease course. As uncontrolled intestinal inflammation can result in severe disease complications, recent treatment targets of IBD evolved toward seeking the absence of mucosal and histological inflammation. However, this approach requires adequate histological evaluation of IBD disease activity. The diagnostic challenge of histological examination of intestinal inflammation is documented by the multitude of proposed histological scoring systems. In this context, we review quantitative phase imaging (QPI) techniques such as digital holographic microscopy (DHM) for characterizing intestinal inflammation. DHM determines optical path-length delays in a stain-free manner, thereby providing the tissue refractive index as a biophysical marker that directly correlates to tissue density. Recently, DHM has been successfully applied in cell biology, cancer cell research and infectious-induced cellular alterations. We summarized the capabilities of DHM and related QPI techniques to assess the severity of intestinal inflammation in experimental colitis as well as in colonic samples from human IBD patients. Moreover, we illustrate major advantages of DHM facilitated multimodal evaluation of epithelial wound healing processes as assessed by physical parameters like cell volume, density, thickness and dry mass in vitro. Furthermore, potential limitations of DHM and future utilities of QPI are discussed. In conclusion, DHM represents a promising, easy-to-use quantitative tool to provide accurate and objective assessment of intestinal inflammation and may pave the way towards automated label-free digital pathology and related in vitro cell culture analysis in future.

Improving cellular analysis throughput of lens-free holographic microscopy with circular Hough transform and convolutional neural networks

Quantitative phase imaging (QPI) became an important technique for label-free biomedical imaging suitable particularly for observation of live cell and dry-mass profiling. Extension of this technique to objects immersed in turbid medium is highly desirable with respect to the need of non-invasive observation of live cells in real 3D environments. Coherencecontrolled holographic microscopy is capable of QPI through turbid media owing to coherence gating induced in transmitted-light geometry by low spatial coherence of illumination. Using this approach, QPI of object in turbid medium can be formed both by ballistic and multiply scattered photons. Moreover, the particular QPIs formed by ballistic and scattered photons can be superimposed thus yielding synthetic QPI of substantially improved image quality. We support the theoretical reasoning of the effect by experimental data.

A cellular-level study of the pathophysiology is crucial for understanding the mechanisms behind human diseases. Recent advances in quantitative phase imaging (QPI) techniques show promises for the cellular-level understanding of the pathophysiology of diseases. To provide important insight on how the QPI techniques potentially improve the study of cell pathophysiology, here we present the principles of QPI and highlight some of the recent applications of QPI ranging from cell homeostasis to infectious diseases and cancer.

Digital in-line holographic microscopy (DIHM) enables efficient and cost-effective computational quantitative phase imaging with a large field of view, making it valuable for studying cell motility, migration, and bio-microfluidics. However, the quality of DIHM reconstructions is compromised by twin-image noise, posing a significant challenge. Conventional methods for mitigating this noise involve complex hardware setups or time-consuming algorithms with often limited effectiveness. In this work, we propose UTIRnet, a deep learning solution for fast, robust, and universally applicable twin-image suppression, trained exclusively on numerically generated datasets. The availability of open-source UTIRnet codes facilitates its implementation in various DIHM systems without the need for extensive experimental training data. Notably, our network ensures the consistency of reconstruction results with input holograms, imparting a physics-based foundation and enhancing reliability compared to conventional deep learning approaches. Experimental verification was conducted among others on live neural glial cell culture migration sensing, which is crucial for neurodegenerative disease research.

Biological cells are composed primarily of water; and as such are challenging to image without staining since the induced intensity modulation of transmitted or reflected light is typically insufficient to permit acceptable contrast for optical imaging. This issue may be resolved with the aid of exogenous contrast agents, but this often has a deleterious effect on the cell and precludes in vivo imaging. A unique approach to this problem is afforded by the phase contrast microscope in which optical-path differences in transmitted light is exploited as a contrast mechanism for qualitative imaging. In recent years however, several quantitative phase imaging techniques have been developed which allow for diffraction limited endogenous-contrast imaging with excellent temporal resolution. We hereby present a laser scanning technique for quantitative phase imaging which achieves sub-diffraction limited resolution at the expense of temporal resolution. This instrument is based on a stabilized fiber interfometer which is incorporated into a near-field scanning optical microscope (NSOM) for tri-modal imaging. Our latest results will focus on modifications made to this system to facilitate imaging in a liquid environment. A simple approach for achieving stable shear-force feedback operation in a liquid will be presented. Acquired high resolution images of white blood cells revealed detailed sub-cellular features. Images of fibroblast cells in air and in a liquid environment confirm the efficacy of the feedback operation in a liquid. Moreover, we demonstrate cell refractometry capability without the need for ad hoc modifications. These results clearly highlight the unique potential of this instrument for the study of living cells.

Low coherence of the illumination substantially improves the quality of holographic and quantitative phase imaging (QPI) by elimination of the coherence noise and various artefacts and by improving the lateral resolution compared to the coherent holographic microscopy. Attributes of coherence-controlled holographic microscope (CCHM) designed and built as an off-axis holographic system allowing QPI within the range from complete coherent to incoherent illumination confirmed these expected advantages. Low coherence illumination also furnishes the coherence gating which constraints imaging of some spatial frequencies of an object axially thus forming an optical section in the wide sense. In this way the depth discrimination capability of the microscope is introduced at the price of restricting the axial interval of possible numerical refocusing. We describe theoretically these effects for the whole range of illumination coherence. We also show that the axial refocusing constraints can be overcome using advanced mode of imaging based on mutual lateral shift of reference and object image fields in CCHM. Lowering the spatial coherence of illumination means increasing its numerical aperture. We study how this change of the illumination geometry influences 3D objects QPI and especially the interpretation of live cells QPI in terms of the dry mass density measurement. In this way a strong dependence of the imaging process on the light coherence is demonstrated. The theoretical calculations and numerical simulations are supported by experimental data including a chance of time-lapse watching of live cells even in optically turbid milieu.

We report the characterization of all the relevant biomechanical properties of individual red blood cells with sickle cell disease using non-invasive quantitative phase imaging and spectroscopy techniques with a previously-validated RBC membrane model.

This paper introduces a procedure aimed to quantitatively measure the optical properties of nanoparticles, namely the complex polarizability and the extinction, scattering, and absorption cross sections, simultaneously. The method is based on the processing of intensity and wavefront images of a light beam illuminating the nanoparticle of interest. Intensity and wavefront measurements are carried out using quadriwave lateral shearing interferometry, a quantitative phase imaging technique with high spatial resolution and sensitivity. The method does not require any preknowledge on the particle and involves a single interferogram image acquisition. The full determination of the actual optical properties of nanoparticles is of particular interest in plasmonics and nanophotonics for the active search and characterization of new materials, e.g., aimed to replace noble metals in future applications of nanoplasmonics with less-lossy or refractory materials.

We present quantitative optical measurements of individual human red blood cells from both diabetes patients and healthy blood donors using 3-D quantitative phase imaging technique in a noninvasive manner.

Interaction between intracellular compartments is based on complex vesicular transport processes. Fluorescence based techniques now reach single molecule resolution in living cells. To avoid fluorophore photobleaching limitations, quantitative phase imaging techniques are conventionally used to produce long-term high contrast cell images. We used an improved wave front sensing set-up called QWLSI-HD, which resolution is high enough to reach nanometric resolution for vesicle localization. We also added specificity to quantitative phase imaging by training artificial intelligence algorithms to recognize intracellular vesicles. We compared performances between the algorithms and also between fixed and living samples.

Motility, or co-ordinated movement, of cells is fundamental for the development of many processes, such as formation of the embryo, the immune response, inflammation, wound healing, and metastasis of cancer cells 1. Cells often migrate in response to specific external signals, but they can also move spontaneously. Aberrant cell motility can be fatal in cancer diseases when cells start to metastasize 2. Metastasis is strictly associated with tissue invasion of the primary tumor cells, and occurs as a multistep progress 3. The first phase of cancer cell metastasis involves the physical translocation of the cell to a distant organ, whereas the second phase implicates the ability of the cancer cell to develop into a metastatic lesion at that distant site 4. For skin cancer melanoma, the main cause of death is widespread metastases 5. Melanoma cells may travel along external vessel lattices. After settling in the metastatic sites, melanoma cells develop mechanisms that protect them against the attack of the immune system. It is, therefore, of great interest and importance to investigate, monitor, and understand the principles of tumor cell invasion and migration. The development of novel therapeutic applications that have the ability to block migratory processes is crucial. For in vitro studies, the cell culture wound-closure, and the transwell migration and invasion assays can provide data for an understanding how well a particular cell type can migrate 6. The wound healing assay is also called a scratch assay because it is performed by making a scratch in the cell monolayer (Fig. 1A). The transwell migration assay is a commonly used test to study the migratory response of endothelial cells to angiogenic inducers or inhibitors (Fig. 1B). This assay is also known as the Boyden or modified Boyden chamber assay. These assays have been frequently used to study movement of cells. Weckmann et al. developed an interesting system to monitor and quantify neutrophils on single cell level, by utilizing commercially available tissue culture hardware, simple video microscopic equipment, and standardized tracking 7. However, the interest for novel standardized real-time analyses using quantitative phase imaging (QPI) for cell tracking is growing (Fig. 2). More than 10 years ago, the digital holographic (DH) microscopy methodology of QPI became known to a larger audience and the technique has since then successfully been applied for label-free monitoring of live cells undergoing cell division, cell proliferation, cell death, and cell migration over time 8-10. By QPI, studies associated with both cellular thickness and refractive index fluctuations have been performed. The possibilities for utilizing QPI for cancer diagnostics have increased 11. Cellular behavior and phenotypes are other parameters that can be measured 12. For two human osteosarcoma cell types, the motility pattern, but not the proliferative pattern, was different. Early migration studies using DH microscopy showed fibroblast migration 13 and HT-1080 fibrosarcoma cells embedded in a 3D collagen gel 14. Alm et al. and Persson et al. also presented data on movement of different cell types and cell sizes 15 as well as demonstrated the correlation of cell movement with cell morphology 16. In the recent article published in the November 2018 issue of Cytometry Part A by Zhang et al., (pages 1125–1131) commercially available DH cytometry platforms equipped with semi-automated image acquisition, segmentation, and analysis software packages for assessing cell behavior are used and discussed. The motility data was obtained with QPI/cytometry using "Track cells module" and "Wound healing module," respectively, and with transwell migration assays determining migration and invasion, respectively. The different techniques assessing motility were compared. The two melanoma cell lines, WM793 and 1205Lu, used in the study were reported to have different metastatic capacity, resulting in differences in proliferation and motility. The motility measured with the "Track cells module" and "Wound healing module," using DH cytometry equipment housed in an incubator, produced highly correlated relative motilities, even when compared to the standard transwell migration and invasion assays. Images acquired with DH are from the same position in a cell culture vessel, making it possible to study individual cells. This is a strong advantage, since most studies of effects of new drugs on proliferation and migration of cancer cells in culture are performed on a population level. In a recent study by Kamlund et al., cell images were captured every fifth minute for a total of up to 72 h 17. For cell movement studies, the semi-automated algorithm attempts to find each tracked cell in the next frame by selecting the closest cell based on the centroid position. The advantages of the Track cells and Wound healing modules over the transwell migration and invasion assays in the paper by Zhang et al., included the possibility to use the cells in the experiment for other purposes after completing the measurement. DH microscopy also benefits from the fact that morphology analysis can be performed of each cell. Indeed, this opens up for almost unlimited possibilities to perform cell morphology analysis using the QPI methodology, since each image is very rich in cellular information. As discussed in a review by El-Schich et al., automated analysis and machine learning is one approach to handle the large amount of morphological data that can now be generated when analyzing cells with QPI 8. Only the computer resources and the training speed will set the limitations.

Quantitative phase imaging (QPI) technique is used to determine various biophysical parameters, such as refractive index, cell thickness, morphology, etc. On the other hand, fluorescence microscopy is used to acquire information regarding molecular specificity of the biological cells and tissues. Conventionally, a fully coherent light source such as laser is used in QPI technique to obtain the interference fringes with ease; however, its high coherence is also responsible for the generation of speckle and spurious fringes, which results in degraded image quality and affects the phase measurement results too. In this paper, we report a multi-modal system that can be effectively utilized to acquire time varied diverse information about the biological specimen with high spatial phase sensitivity. Herein, a single unit comprising of a fluorescence microscope and the Linnik based interferometer specially equipped with a partially spatially coherent light source illumination was developed. The integrated system is capable to procure molecular specificity and phase information of biological specimen, in a single shot, utilizing a single-chip color CCD camera. Here, we performed experiments on MG63 osteosarcoma cells, and the composite interferometric-fluorescence images were obtained and then digitally decomposed into red and green colors; and, the phase maps were reconstructed using the Fourier fringe analysis method. Furthermore, the cultured cells were monitored over a time-span to observe and investigate the time dependent morphological changes along with the quantification of cellular adhesion and spreading. Hence, the proposed system can be utilized to quantify time dependent changes in the cell’s morphology and in cell adhesion which can be an indicator for the detection of various range of diseases such as arthritis, cancer, osteoporosis and atherosclerosis.