Three-dimensional label-free imaging and quantification of lipid droplets in live hepatocytes

Label-free three-dimensional imaging and quantitative analysis of living fibroblasts and myofibroblasts by holotomographic microscopy

Holotomography (HT) is a cutting-edge fast live-cell quantitative label-free imaging technique. Based on the principle of quantitative phase imaging, it combines holography and tomography to record a three-dimensional map of the refractive index, used as intrinsic optical and quantitative imaging contrast parameter of biological samples, at a sub-micrometer spatial resolution. In this study HT has been employed for the first time to analyze the changes of fibroblasts differentiating towards myofibroblasts - recognized as the main cell player of fibrosis - when cultured in vitro with the pro-fibrotic factor, namely transforming growth factor-β1. In parallel, F-actin, vinculin, α-smooth muscle actin, phospho-myosin light chain 2, type-1 collagen, peroxisome proliferator-activated receptor-gamma coactivator-1α expression and mitochondria were evaluated by confocal laser scanning microscopy. Plasmamembrane passive properties and transient receptor potential canonical channels' currents were also recorded by whole-cell patch-clamp. The fluorescence images and electrophysiological results have been compared to the data obtained by HT and their congruence has been discussed. HT turned out to be a valid approach to morphologically distinguish fibroblasts from well differentiated myofibroblasts while obtaining objective measures concerning volume, surface area, projection area, surface index and dry mass (i.e., the mass of the non-aqueous content inside the cell including proteins and subcellular organelles) of the entire cell, nuclei and nucleoli with the major advantage to monitor outer and inner features in living cells in a non-invasive, rapid and label-free approach. HT might open up new research opportunities in the field of fibrotic diseases. RESEARCH HIGHLIGHTS: Holotomography (HT) is a label-free laser interferometric imaging technology exploiting the intrinsic optical property of cells namely refractive index (RI) to enable a direct imaging and analysis of whole cells or intracellular organelles. HT turned out a valid approach to distinguish morphological features of living unlabeled fibroblasts from differentiated myofibroblasts. HT provided quantitative information concerning volume, surface area, projection area, surface index and dry mass of the entire fibroblasts/myofibroblasts, nuclei and nucleoli.

Label-free morpho-molecular phenotyping of living cancer cells by combined Raman spectroscopy and phase tomography

Accurate, rapid and non-invasive cancer cell phenotyping is a pressing concern across the life sciences, as standard immuno-chemical imaging and omics require extended sample manipulation. Here we combine Raman micro-spectroscopy and phase tomography to achieve label-free morpho-molecular profiling of human colon cancer cells, following the adenoma, carcinoma, and metastasis disease progression, in living and unperturbed conditions. We describe how to decode and interpret quantitative chemical and co-registered morphological cell traits from Raman fingerprint spectra and refractive index tomograms. Our multimodal imaging strategy rapidly distinguishes cancer phenotypes, limiting observations to a low number of pristine cells in culture. This synergistic dataset allows us to study independent or correlated information in spectral and tomographic maps, and how it benefits cell type inference. This method is a valuable asset in biomedical research, particularly when biological material is in short supply, and it holds the potential for non-invasive monitoring of cancer progression in living organisms.

Applicability of non-invasive and live-cell holotomographic imaging on fungi

The ability to acquire three-dimensional (3D) information of cellular structures without the need for fluorescent tags or staining makes holotomographic imaging a powerful tool in cellular biology. It provides valuable insights by measuring the refractive index (RI), an optical parameter describing the phase delay of light that passes through the living cell. Here, we demonstrate holotomographic imaging on industrial relevant ascomycete fungi and study their development and morphogenesis. This includes conidial germination, subcellular dynamics, and cytoplasmic flow during hyphal growth in Aspergillus niger. In addition, growth and budding of Aureobasidium pullulans cells are captured using holotomographic microscopy. Coupled to fluorescence imaging, lipid droplets, vacuoles, the mitochondrial network, and nuclei are targeted and analyzed in the 3D RI reconstructed images. While lipid droplets and vacuoles can be assigned to a specific RI pattern, mitochondria and nuclei were not pronounced. We show, that the lower sensitivity of RI measurements derives from the fungal cell wall that acts as an additional barrier for the illumination light of the microscope. After cell wall digest of hyphae and protoplast formation of A. niger expressing GFP-tagged histone H2A, location of nuclei could be determined by non-invasive RI measurements. Furthermore, we used coupled fluorescence microscopy to observe migration of nuclei in unperturbed hyphal segments and duplication during growth on a single-cell level. Detailed micromorphological studies in Saccharomyces cerevisiae and Trichoderma reesei are challenging due to cell size restrictions. Overall, holotomography opens up new avenues for exploring dynamic cellular processes in real time and enables the visualization of fungi from a new perspective.

Quantitative phase imaging based on holography: trends and new perspectives

In 1948, Dennis Gabor proposed the concept of holography, providing a pioneering solution to a quantitative description of the optical wavefront. After 75 years of development, holographic imaging has become a powerful tool for optical wavefront measurement and quantitative phase imaging. The emergence of this technology has given fresh energy to physics, biology, and materials science. Digital holography (DH) possesses the quantitative advantages of wide-field, non-contact, precise, and dynamic measurement capability for complex-waves. DH has unique capabilities for the propagation of optical fields by measuring light scattering with phase information. It offers quantitative visualization of the refractive index and thickness distribution of weak absorption samples, which plays a vital role in the pathophysiology of various diseases and the characterization of various materials. It provides a possibility to bridge the gap between the imaging and scattering disciplines. The propagation of wavefront is described by the complex amplitude. The complex-value in the complex-domain is reconstructed from the intensity-value measurement by camera in the real-domain. Here, we regard the process of holographic recording and reconstruction as a transformation between complex-domain and real-domain, and discuss the mathematics and physical principles of reconstruction. We review the DH in underlying principles, technical approaches, and the breadth of applications. We conclude with emerging challenges and opportunities based on combining holographic imaging with other methodologies that expand the scope and utility of holographic imaging even further. The multidisciplinary nature brings technology and application experts together in label-free cell biology, analytical chemistry, clinical sciences, wavefront sensing, and semiconductor production.

Convolutional neural network model for automatic recognition and classification of pancreatic cancer cell based on analysis of lipid droplet on unlabeled sample by 3D optical diffraction tomography

INTRODUCTION

Pancreatic cancer cells generally accumulate large numbers of lipid droplets (LDs), which regulate lipid storage. To promote rapid diagnosis, an automatic pancreatic cancer cell recognition system based on a deep convolutional neural network was proposed in this study using quantitative images of LDs from stain-free cytologic samples by optical diffraction tomography.

METHODS

We retrieved 3D refractive index tomograms and reconstructed 37 optical images of one cell. From the four cell lines, the obtained fields were separated into training and test datasets with 10,397 and 3,478 images, respectively. Furthermore, we adopted several machine learning techniques based on a single image-based prediction model to improve the performance of the computer-aided diagnostic system.

RESULTS

Pancreatic cancer cells had a significantly lower total cell volume and dry mass than did normal pancreatic cells and were accompanied by greater numbers of lipid droplets (LDs). When evaluating multitask learning techniques utilizing the EfficientNet-b3 model through confusion matrices, the overall 2-category accuracy for cancer classification reached 96.7 %. Simultaneously, the overall 4-category accuracy for individual cell line classification achieved a high accuracy of 96.2 %. Furthermore, when we added the core techniques one by one, the overall performance of the proposed technique significantly improved, reaching an area under the curve (AUC) of 0.997 and an accuracy of 97.06 %. Finally, the AUC reached 0.998 through the ablation study with the score fusion technique.

DISCUSSION

Our novel training strategy has significant potential for automating and promoting rapid recognition of pancreatic cancer cells. In the near future, deep learning-embedded medical devices will substitute laborious manual cytopathologic examinations for sustainable economic potential.

Monitoring the Interaction Between Solid Lipid Nanoparticles and Alveolar Macrophages Via the Label-Free Technique

Macrophages are employed as targets for delivering genes, drugs, or lipid nanoparticles into tumors or other specific sites. Studying the interaction between solid lipid nanoparticles (SLNs) and macrophages is essential for assessing nanotoxicity and advancing the development of nanomedicines. However, limited data are currently available on the membrane microstructure and biochemical changes that occur when macrophages interact with SLNs. We conducted a label-free morphological and biochemical investigation of NR8383 macrophages using optical diffraction tomography (ODT), which validated the efficiency of the SLNs as a drug delivery system. ODT provided intracellular holotomography to characterize the macrophages and fluorescence imaging to analyze delivery efficiency. ODT analysis revealed the responses of phagocytic macrophages. Additionally, a quantitative analysis of lipid droplets using refractive indices revealed that, compared with incubation with normal cells, incubation with SLNs significantly increased the lipid droplet volume and surface area. The uptake of SLNs into macrophages resulted in increased cell volume, surface area, and concentration, which indicated greater morphological and biochemical variability in the treated cells than in the control cells. The results suggest that ODT imaging is promising for understanding the intracellular distribution of SLNs and useful for validating the efficacy of delivery of SLNs to macrophages.

Recent Advances and Current Trends in Transmission Tomographic Diffraction Microscopy

Optical microscopy techniques are among the most used methods in biomedical sample characterization. In their more advanced realization, optical microscopes demonstrate resolution down to the nanometric scale. These methods rely on the use of fluorescent sample labeling in order to break the diffraction limit. However, fluorescent molecules' phototoxicity or photobleaching is not always compatible with the investigated samples. To overcome this limitation, quantitative phase imaging techniques have been proposed. Among these, holographic imaging has demonstrated its ability to image living microscopic samples without staining. However, for a 3D assessment of samples, tomographic acquisitions are needed. Tomographic Diffraction Microscopy (TDM) combines holographic acquisitions with tomographic reconstructions. Relying on a 3D synthetic aperture process, TDM allows for 3D quantitative measurements of the complex refractive index of the investigated sample. Since its initial proposition by Emil Wolf in 1969, the concept of TDM has found a lot of applications and has become one of the hot topics in biomedical imaging. This review focuses on recent achievements in TDM development. Current trends and perspectives of the technique are also discussed.

Enhanced functionalities of immune cells separated by a microfluidic lattice: assessment based on holotomography

The isolation of white blood cells (WBCs) from whole blood constitutes a pivotal process for immunological studies, diagnosis of hematologic disorders, and the facilitation of immunotherapy. Despite the ubiquity of density gradient centrifugation in WBC isolation, its influence on WBC functionality remains inadequately understood. This research employs holotomography to explore the effects of two distinct WBC separation techniques, namely conventional centrifugation and microfluidic separation, on the functionality of the isolated cells. We utilize three-dimensional refractive index distribution and time-lapse dynamics to analyze individual WBCs in-depth, focusing on their morphology, motility, and phagocytic capabilities. Our observations highlight that centrifugal processes negatively impact WBC motility and phagocytic capacity, whereas microfluidic separation yields a more favorable outcome in preserving WBC functionality. These findings emphasize the potential of microfluidic separation techniques as a viable alternative to traditional centrifugation for WBC isolation, potentially enabling more precise analyses in immunology research and improving the accuracy of hematologic disorder diagnoses.

Noninvasive morpho-molecular imaging reveals early therapy-induced senescence in human cancer cells

Anticancer therapy screening in vitro identifies additional treatments and improves clinical outcomes. Systematically, although most tested cells respond to cues with apoptosis, an appreciable portion enters a senescent state, a critical condition potentially driving tumor resistance and relapse. Conventional screening protocols would strongly benefit from prompt identification and monitoring of therapy-induced senescent (TIS) cells in their native form. We combined complementary all-optical, label-free, and quantitative microscopy techniques, based on coherent Raman scattering, multiphoton absorption, and interferometry, to explore the early onset and progression of this phenotype, which has been understudied in unperturbed conditions. We identified TIS manifestations as early as 24 hours following treatment, consisting of substantial mitochondrial rearrangement and increase of volume and dry mass, followed by accumulation of lipid vesicles starting at 72 hours. This work holds the potential to affect anticancer treatment research, by offering a label-free, rapid, and accurate method to identify initial TIS in tumor cells.

Influence of Chemical and Genetic Manipulations on Cellular Organelles Quantified by Label-Free Optical Diffraction Tomography

Label-free optical diffraction tomography provides three-dimensional imaging of cells and organelles, along with their refractive index (RI) and volume. These physical parameters are valuable for quantitative and accurate analysis of the subcellular microenvironment and its connections to intracellular biological properties. In biological and biochemical cell analysis, various invasive cell manipulations are used, such as temperature change, chemical fixation, live cell staining with fluorescent dye, and gene overexpression of exogenous proteins. However, it is not fully understood how these various manipulations affect the physicochemical properties of different organelles. In this study, we investigated the impact of these manipulations on the cellular properties of single HeLa cells. We found that after cell fixation and an increase in temperature, the RI value of organelles, such as the nucleus and cytoplasm, significantly decreased overall. Interestingly, unlike the cell nuclei, cytoplasmic RI values were hardly detected after membrane permeation, indicating that only intracytoplasmic components were largely lost. Additionally, our findings revealed that the expression of GFP and GFP-tagged proteins significantly increased the RI values of organelles in living cells compared to the less effective RI changes observed with chemical fluorescence staining for cell organelles. The result demonstrates that distinct types of invasive manipulations can alter the microenvironment of organelles in different ways. Our study sheds new light on how chemical and genetic manipulations affect organelles.

Scattered-light-sheet microscopy with sub-cellular resolving power

Since its first demonstration over 100 years ago, scattering-based light-sheet microscopy has recently re-emerged as a key modality in label-free tissue imaging and cellular morphometry; however, scattering-based light-sheet imaging with subcellular resolution remains an unmet target. This is because related approaches inevitably superimpose speckle or granular intensity modulation on to the native subcellular features. Here, we addressed this challenge by deploying a time-averaged pseudo-thermalized light-sheet illumination. While this approach increased the lateral dimensions of the illumination sheet, we achieved subcellular resolving power after image deconvolution. We validated this approach by imaging cytosolic carbon depots in yeast and bacteria with increased specificity, no staining, and ultralow irradiance levels. Overall, we expect this scattering-based light-sheet microscopy approach will advance single, live cell imaging by conferring low-irradiance and label-free operation towards eradicating phototoxicity.

Squid leucophore-inspired engineering of optically dynamic human cells

Cephalopods (e.g., squids, octopuses, and cuttlefishes) possess remarkable dynamic camouflage abilities and therefore have emerged as powerful sources of inspiration for the engineering of dynamic optical technologies. Within this context, we have focused on the development of engineered living systems that can emulate the tunable optical characteristics of some squid skin cells. Herein, we expand our ability to controllably incorporate reflectin-based structures within mammalian cells via genetic engineering methods, and demonstrate that such structures can facilitate holotomographic and standard microscopy imaging of the cells. Moreover, we show that the reflectin-based structures within our cells can be reconfigured with a straightforward chemical stimulus, and we quantify the stimulus-induced changes observed for the structures at the single cell level. The reported findings may enable a better understanding of the color- and appearance-changing capabilities of some cephalopod skin cells and could afford opportunities for reflectins as molecular probes in the fields of cell biology and biomedical optics.

Influence of Yokukansan on the refractive index of neuroblastoma cells

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.

In-silico clearing approach for deep refractive index tomography by partial reconstruction and wave-backpropagation

Refractive index (RI) is considered to be a fundamental physical and biophysical parameter in biological imaging, as it governs light-matter interactions and light propagation while reflecting cellular properties. RI tomography enables volumetric visualization of RI distribution, allowing biologically relevant analysis of a sample. However, multiple scattering (MS) and sample-induced aberration (SIA) caused by the inhomogeneity in RI distribution of a thick sample make its visualization challenging. This paper proposes a deep RI tomographic approach to overcome MS and SIA and allow the enhanced reconstruction of thick samples compared to that enabled by conventional linear-model-based RI tomography. The proposed approach consists of partial RI reconstruction using multiple holograms acquired with angular diversity and their backpropagation using the reconstructed partial RI map, which unambiguously reconstructs the next partial volume. Repeating this operation efficiently reconstructs the entire RI tomogram while suppressing MS and SIA. We visualized a multicellular spheroid of diameter 140 µm within minutes of reconstruction, thereby demonstrating the enhanced deep visualization capability and computational efficiency of the proposed method compared to those of conventional RI tomography. Furthermore, we quantified the high-RI structures and morphological changes inside multicellular spheroids, indicating that the proposed method can retrieve biologically relevant information from the RI distribution. Benefitting from the excellent biological interpretability of RI distributions, the label-free deep visualization capability of the proposed method facilitates a noninvasive understanding of the architecture and time-course morphological changes of thick multicellular specimens.

Single-shot refractive index slice imaging using spectrally multiplexed optical transfer function reshaping

The refractive index (RI) of cells and tissues is crucial in pathophysiology as a noninvasive and quantitative imaging contrast. Although its measurements have been demonstrated using three-dimensional quantitative phase imaging methods, these methods often require bulky interferometric setups or multiple measurements, which limits the measurement sensitivity and speed. Here, we present a single-shot RI imaging method that visualizes the RI of the in-focus region of a sample. By exploiting spectral multiplexing and optical transfer function engineering, three color-coded intensity images of a sample with three optimized illuminations were simultaneously obtained in a single-shot measurement. The measured intensity images were then deconvoluted to obtain the RI image of the in-focus slice of the sample. As a proof of concept, a setup was built using Fresnel lenses and a liquid-crystal display. For validation purposes, we measured microspheres of known RI and cross-validated the results with simulated results. Various static and highly dynamic biological cells were imaged to demonstrate that the proposed method can conduct single-shot RI slice imaging of biological samples with subcellular resolution.

Using mass spectrometry imaging to visualize age-related subcellular disruption

Metabolic homeostasis balances the production and consumption of energetic molecules to maintain active, healthy cells. Cellular stress, which disrupts metabolism and leads to the loss of cellular homeostasis, is important in age-related diseases. We focus here on the role of organelle dysfunction in age-related diseases, including the roles of energy deficiencies, mitochondrial dysfunction, endoplasmic reticulum (ER) stress, changes in metabolic flux in aging (e.g., Ca2+ and nicotinamide adenine dinucleotide), and alterations in the endoplasmic reticulum-mitochondria contact sites that regulate the trafficking of metabolites. Tools for single-cell resolution of metabolite pools and metabolic flux in animal models of aging and age-related diseases are urgently needed. High-resolution mass spectrometry imaging (MSI) provides a revolutionary approach for capturing the metabolic states of individual cells and cellular interactions without the dissociation of tissues. mass spectrometry imaging can be a powerful tool to elucidate the role of stress-induced cellular dysfunction in aging.

Optical trapping with holographically structured light for single-cell studies

A groundbreaking work in 1970 by Arthur Ashkin paved the way for developing various optical trapping techniques. Optical tweezers have become an established method for the manipulation of biological objects, due to their noninvasiveness and precise controllability. Recent innovations are accelerating and now enable single-cell manipulation through holographic light structuring. In this review, we provide an overview of recent advances in optical tweezer techniques for studies at the individual cell level. Our review focuses on holographic optical tweezers that utilize active spatial light modulators to noninvasively manipulate live cells. The versatility of the technology has led to valuable integrations with microscopy, microfluidics, and biotechnological techniques for various single-cell studies. We aim to recapitulate the basic principles of holographic optical tweezers, highlight trends in their biophysical applications, and discuss challenges and future prospects.

Light distribution in fat cell layers at physiological temperatures

Adipose tissue (AT) optical properties for physiological temperatures and in vivo conditions are still insufficiently studied. The AT is composed mainly of packed cells close to spherical shape. It is a possible reason that AT demonstrates a very complicated spatial structure of reflected or transmitted light. It was shown with a cellular tissue phantom, is split into a fan of narrow tracks, originating from the insertion point and representing filament-like light distribution. The development of suitable approaches for describing light propagation in a AT is urgently needed. A mathematical model of the propagation of light through the layers of fat cells is proposed. It has been shown that the sharp local focusing of optical radiation (light localized near the shadow surface of the cells) and its cleavage by coupling whispering gallery modes depends on the optical thickness of the cell layer. The optical coherence tomography numerical simulation and experimental studies results demonstrate the importance of sharp local focusing in AT for understanding its optical properties for physiological conditions and at AT heating.

Standardizing image assessment in optical diffraction tomography

Optical diffraction tomography (ODT) has gradually become a popular label-free imaging technique that offers diffraction-limited resolution by mapping an object's three-dimensional (3D) refractive index (RI) distribution. However, there is a lack of comprehensive quantitative image assessment metrics in ODT for studying how various experimental conditions influence image quality, and subsequently optimizing the experimental conditions. In this Letter, we propose to standardize the image assessment in ODT by proposing a set of metrics, including signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and structural distinguishability (SD). To test the feasibility of the metrics, we performed experiments on angle-scanning ODT by varying the number of illumination angles, RI contrast of samples, sample feature sizes, and sample types (e.g., standard polystyrene beads and 3D printed structures) and evaluated the RI tomograms with SNR, CNR, and SD. We further quantitatively studied how image quality can be improved, and tested the image assessment metrics on subcellular structures of living cells. We envision the proposed image assessment metrics may greatly benefit end-users for assessing the RI tomograms, as well as experimentalists for optimizing ODT instruments.

Lack of Nck1 protein and Nck-CD3 interaction caused the increment of lipid content in Jurkat T cells

Background

The non-catalytic region of tyrosine kinase (Nck) is an adaptor protein, which is ubiquitously expressed in many types of cells. In T cells, the Nck1 isoform promotes T cell receptor signalling as well as actin polymerisation. However, the role of Nck1 in the lipid metabolism in T cells is unknown. In the present study, we investigated the effect of the Nck1 protein and Nck–CD3 interaction on lipid metabolism and on the physical and biological properties of Jurkat T cells, using a newly developed holotomographic microscope.

Results

Holotomographic microscopy showed that Nck1-knocked-out cells had membrane blebs and were irregular in shape compared to the rounded control cells. The cell size and volume of Nck1-deficient cells were comparable to those of the control cells. Nck1-knocked-out Jurkat T cells had a greater lipid content, lipid mass/cell mass ratio, and lipid metabolite levels than the control cells. Interestingly, treatment with a small molecule, AX-024, which inhibited Nck–CD3 interaction, also caused an increase in the lipid content in wild-type Jurkat T cells, as found in Nck1-deficient cells.

Conclusions

Knockout of Nck1 protein and hindrance of the Nck–CD3 interaction cause the elevation of lipid content in Jurkat T cells.

Stain-free identification of cell nuclei using tomographic phase microscopy in flow cytometry

Quantitative Phase Imaging (QPI) has gained popularity in bioimaging because it can avoid the need for cell staining, which in some cases is difficult or impossible. However, as a result, QPI does not provide labelling of various specific intracellular structures. Here we show a novel computational segmentation method based on statistical inference that makes it possible for QPI techniques to identify the cell nucleus. We demonstrate the approach with refractive index tomograms of stain-free cells reconstructed through the tomographic phase microscopy in flow cytometry mode. In particular, by means of numerical simulations and two cancer cell lines, we demonstrate that the nucleus can be accurately distinguished within the stain-free tomograms. We show that our experimental results are consistent with confocal fluorescence microscopy (FM) data and microfluidic cytofluorimeter outputs. This is a significant step towards extracting specific three-dimensional intracellular structures directly from the phase-contrast data in a typical flow cytometry configuration.

Quantitative Phase Imaging Detecting the Hypoxia-Induced Patterns in Healthy and Neoplastic Human Colonic Epithelial Cells

Hypoxia is a frequent phenomenon during carcinogenesis and may lead to functional and structural changes in proliferating cancer cells. Colorectal cancer (CRC) is one of the most common neoplasms in which hypoxia is associated with progression. The aim of this study was to assess the optical parameters and microanatomy of CRC and the normal intestinal epithelium cells using the digital holotomography (DHT) method. The examination was conducted on cancer (HT-29, LoVo) and normal colonic cells (CCD-18Co) cultured in normoxic and hypoxic environments. The assessment included optical parameters such as the refractive index (RI) and dry mass as well as the morphological features. Hypoxia decreased the RI in all cells as well as in their cytoplasm, nucleus, and nucleoli. The opposite tendency was noted for spheroid-vesicular structures, where the RI was higher for the hypoxic state. The total volume of hypoxic CCD-18Co and LoVo cells was decreased, while an increase in this parameter was observed for HT-29 cells. Hypoxia increased the radius and cell volume, including the dry mass of the vesicular content. The changes in the optics and morphology of hypoxic cells may suggest the possibility of using DHT in the detection of circulating tumor cells (CTCs).

Finding intracellular lipid droplets from the single-cell biolens' signature in a holographic flow-cytometry assay

In recent years, intracellular LDs have been discovered to play an important role in several pathologies. Therefore, detection of LDs would provide an in-demand diagnostic tool if coupled with flow-cytometry to give significant statistical analysis and especially if the diagnosis is made in full non-invasive mode. Here we combine the experimental results of in-flow tomographic phase microscopy with a suited numerical simulation to demonstrate that intracellular LDs can be easily detected through a label-free approach based on the direct analysis of the 2D quantitative phase maps recorded by a holographic flow cytometer. In fact, we demonstrate that the presence of LDs affects the optical focusing lensing features of the embracing cell, which can be considered a biological lens. The research was conducted on white blood cells (i.e., lymphocytes and monocytes) and ovarian cancer cells. Results show that the biolens properties of cells can be a rapid biomarker that aids in boosting the diagnosis of LDs-related pathologies by means of the holographic flow-cytometry assay for fast, non-destructive, and high-throughput screening of statistically significant number of cells.

Alpha-Lipoic Acid Attenuates Apoptosis and Ferroptosis in Cisplatin-Induced Ototoxicity via the Reduction of Intracellular Lipid Droplets

Alpha-lipoic acid (α-LA) is a potent antioxidant that can prevent apoptosis associated with cisplatin-induced ototoxicity through ROS. Ferroptosis is defined as an iron-dependent cell death pathway that has recently been highlighted and is associated with the accumulation of intracellular lipid droplets (LDs) due to an inflammatory process. Herein, we investigated the impact of α-LA on ferroptosis and analyzed the characteristics of LDs in auditory hair cells treated with cisplatin using high-resolution 3D quantitative-phase imaging with reconstruction of the refractive index (RI) distribution. HEI-OC1 cells were treated with 500 μM α-LA for 24 h and then with 15 μM cisplatin for 48 h. With 3D optical diffraction tomography (3D-ODT), the RI values of treated cells were analyzed. Regions with high RI values were considered to be LDs and labelled to measure the count, mass, and volume of LDs. The expression of LC3-B, P62, GPX4, 4-hydroxynonenal (4-HNE), and xCT was evaluated by Western blotting. HEI-OC1 cells damaged by cisplatin showed lipid peroxidation, depletion of xCT, and abnormal accumulation of 4-HNE. Additionally, the count, mass, and volume of LDs increased in the cells. Cells treated with α-LA had inhibited expression of 4-HNE, while the expression of xCT and GPX4 was recovered, which restored LDs to a level that was similar to that in the control group. Our research on LDs with 3D-ODT offers biological evidence of ferroptosis and provides insights on additional approaches for investigating the molecular pathways.

Quantitative Phase Imaging: Recent Advances and Expanding Potential in Biomedicine

Quantitative phase imaging (QPI) is a label-free, wide-field microscopy approach with significant opportunities for biomedical applications. QPI uses the natural phase shift of light as it passes through a transparent object, such as a mammalian cell, to quantify biomass distribution and spatial and temporal changes in biomass. Reported in cell studies more than 60 years ago, ongoing advances in QPI hardware and software are leading to numerous applications in biology, with a dramatic expansion in utility over the past two decades. Today, investigations of cell size, morphology, behavior, cellular viscoelasticity, drug efficacy, biomass accumulation and turnover, and transport mechanics are supporting studies of development, physiology, neural activity, cancer, and additional physiological processes and diseases. Here, we review the field of QPI in biology starting with underlying principles, followed by a discussion of technical approaches currently available or being developed, and end with an examination of the breadth of applications in use or under development. We comment on strengths and shortcomings for the deployment of QPI in key biomedical contexts and conclude with emerging challenges and opportunities based on combining QPI with other methodologies that expand the scope and utility of QPI even further.

Cell Cycle Stage Classification Using Phase Imaging with Computational Specificity

Traditional methods for cell cycle stage classification rely heavily on fluorescence microscopy to monitor nuclear dynamics. These methods inevitably face the typical phototoxicity and photobleaching limitations of fluorescence imaging. Here, we present a cell cycle detection workflow using the principle of phase imaging with computational specificity (PICS). The proposed method uses neural networks to extract cell cycle-dependent features from quantitative phase imaging (QPI) measurements directly. Our results indicate that this approach attains very good accuracy in classifying live cells into G1, S, and G2/M stages, respectively. We also demonstrate that the proposed method can be applied to study single-cell dynamics within the cell cycle as well as cell population distribution across different stages of the cell cycle. We envision that the proposed method can become a nondestructive tool to analyze cell cycle progression in fields ranging from cell biology to biopharma applications.

Simultaneous 3D deconvolution and halo removal for spatial light interference microscopy through a two-edge apodized Wiener filter

As one of the most sensitive quantitative phase microscopy techniques, spatial light interference microscopy (SLIM) has undergone rapid development in the past decade and has seen wide application in both basic science and clinical studies. However, as with any other traditional microscope, the axial resolution is the worst among the three dimensions. This leads to lower contrast in the thicker regions of cell samples. Another common foe in the phase contrast image is the halo artifact, which can block underlying structures, in particular when high resolution is desired. Current solutions focus on either halo removal or contrast enhancement alone, and thus need two processing steps to create both high contrast and halo-free phase images. Further, raw images often suffer from artifacts that are both bright and slowly varying, dubbed here as cloud-like artifacts. After deconvolution, these cloud-like artifacts often dominate the image and obscure high-frequency information, which is typically of greatest interest. In this paper, we first analyzed the unique characteristics of the phase transfer function associated with SLIM to find the root of the cloud-like artifacts and halo artifacts. Then we designed a two-edge apodized deconvolution scheme as a counter measure. We show that even with a simple Wiener filter, the two-edge apodization (TEA) can effectively improve the contrast while suppressing the halo and cloud-like artifacts. Our algorithm, named TEA-Weiner, is non-iterative and thus can be implemented in real time. For low-contrast structures inside the cell such as the endoplasmic reticulum (ER), where ringing artifacts are more likely, we show that two-edge apodization can be combined with additional constraints such as total variation so that their contrast can be enhanced simultaneously with other bright structures inside the cell. Comparing our method with other state-of-the-art algorithms, our method has two advantages: First, deconvolution and halo removal are accomplished simultaneously; second, the image quality is highest using TEA-Weiner filtering.

Interactions of Nanoparticles with Macrophages and Feasibility of Drug Delivery for Asthma

Understanding the interaction between nanoparticles and immune cells is essential for the evaluation of nanotoxicity and development of nanomedicines. However, to date, there is little data on the membrane microstructure and biochemical changes in nanoparticle-loaded immune cells. In this study, we observed the microstructure of nanoparticle-loaded macrophages and changes in lipid droplets using holotomography analysis. Quantitatively analyzing the refractive index distribution of nanoparticle-loaded macrophages, we identified the interactions between nanoparticles and macrophages. The results showed that, when nanoparticles were phagocytized by macrophages, the number of lipid droplets and cell volume increased. The volume and mass of the lipid droplets slightly increased, owing to the absorption of nanoparticles. Meanwhile, the number of lipid droplets increased more conspicuously than the other factors. Furthermore, alveolar macrophages are involved in the development and progression of asthma. Studies have shown that macrophages play an essential role in the maintenance of asthma-related inflammation and tissue damage, suggesting that macrophage cells may be applied to asthma target delivery strategies. Therefore, we investigated the target delivery efficiency of gold nanoparticle-loaded macrophages at the biodistribution level, using an ovalbumin-induced asthma mouse model. Normal and severe asthma models were selected to determine the difference in the level of inflammation in the lung. Consequently, macrophages had increased mobility in models of severe asthma, compared to those of normal asthma disease. In this regard, the detection of observable differences in nanoparticle-loaded macrophages may be of primary interest, as an essential endpoint analysis for investigating nanomedical applications and immunotheragnostic strategies.

Label-free imaging and evaluation of characteristic properties of asthma-derived eosinophils using optical diffraction tomography

Optical diffraction tomography (ODT), an emerging imaging technique that does not require fluorescent staining, can measure the three-dimensional distribution of the refractive index (RI) of organelles. In this study, we used ODT to characterize the pathological characteristics of human eosinophils derived from asthma patients presenting with eosinophilia. In addition to morphological information about organelles appearing in eosinophils, including the cytoplasm, nucleus, and vacuole, we succeeded in imaging specific granules and quantifying the RI values of the granules. Interestingly, ODT analysis showed that the RI (i.e., molecular density) of granules was significantly different between eosinophils from asthma patients and healthy individuals without eosinophilia, and that vacuoles were frequently found in the cells of asthma patients. Our results suggest that the physicochemical properties of eosinophils derived from patients with asthma can be quantitatively distinguished from those of healthy individuals. The method will provide insight into efficient evaluation of the characteristics of eosinophils at the organelle level for various diseases with eosinophilia.

Characterizing Organelles in Live Stem Cells Using Label-Free Optical Diffraction Tomography

Label-free optical diffraction tomography (ODT), an imaging technology that does not require fluorescent labeling or other pre-processing, can overcome the limitations of conventional cell imaging technologies, such as fluorescence and electron microscopy. In this study, we used ODT to characterize the cellular organelles of three different stem cells-namely, human liver derived stem cell, human umbilical cord matrix derived mesenchymal stem cell, and human induced pluripotent stem cell-based on their refractive index and volume of organelles. The physical property of each stem cell was compared with that of fibroblast. Based on our findings, the characteristic physical properties of specific stem cells can be quantitatively distinguished based on their refractive index and volume of cellular organelles. Altogether, the method employed herein could aid in the distinction of living stem cells from normal cells without the use of fluorescence or specific biomarkers.

Learning to see colours: Biologically relevant virtual staining for adipocyte cell images

Fluorescence microscopy, which visualizes cellular components with fluorescent stains, is an invaluable method in image cytometry. From these images various cellular features can be extracted. Together these features form phenotypes that can be used to determine effective drug therapies, such as those based on nanomedicines. Unfortunately, fluorescence microscopy is time-consuming, expensive, labour intensive, and toxic to the cells. Bright-field images lack these downsides but also lack the clear contrast of the cellular components and hence are difficult to use for downstream analysis. Generating the fluorescence images directly from bright-field images using virtual staining (also known as “label-free prediction” and “in-silico labeling”) can get the best of both worlds, but can be very challenging to do for poorly visible cellular structures in the bright-field images. To tackle this problem deep learning models were explored to learn the mapping between bright-field and fluorescence images for adipocyte cell images. The models were tailored for each imaging channel, paying particular attention to the various challenges in each case, and those with the highest fidelity in extracted cell-level features were selected. The solutions included utilizing privileged information for the nuclear channel, and using image gradient information and adversarial training for the lipids channel. The former resulted in better morphological and count features and the latter resulted in more faithfully captured defects in the lipids, which are key features required for downstream analysis of these channels.

Dissecting lipid droplet biology with coherent Raman scattering microscopy

Lipid droplets (LDs) are lipid-rich organelles universally found in most cells. They serve as a key energy reservoir, actively participate in signal transduction and dynamically communicate with other organelles. LD dysfunction has been associated with a variety of diseases. The content level, composition and mobility of LDs are crucial for their physiological and pathological functions, and these different parameters of LDs are subject to regulation by genetic factors and environmental inputs. Coherent Raman scattering (CRS) microscopy utilizes optical nonlinear processes to probe the intrinsic chemical bond vibration, offering label-free, quantitative imaging of lipids in vivo with high chemical specificity and spatiotemporal resolution. In this Review, we provide an overview over the principle of CRS microscopy and its application in tracking different parameters of LDs in live cells and organisms. We also discuss the use of CRS microscopy in genetic screens to discover lipid regulatory mechanisms and in understanding disease-related lipid pathology.

Toward deep biophysical cytometry: prospects and challenges

The biophysical properties of cells reflect their identities, underpin their homeostatic state in health, and define the pathogenesis of disease. Recent leapfrogging advances in biophysical cytometry now give access to this information, which is obscured in molecular assays, with a discriminative power that was once inconceivable. However, biophysical cytometry should go 'deeper' in terms of exploiting the information-rich cellular biophysical content, generating a molecular knowledge base of cellular biophysical properties, and standardizing the protocols for wider dissemination. Overcoming these barriers, which requires concurrent innovations in microfluidics, optical imaging, and computer vision, could unleash the enormous potential of biophysical cytometry not only for gaining a new mechanistic understanding of biological systems but also for identifying new cost-effective biomarkers of disease.

Holographic tomography: techniques and biomedical applications [Invited]

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.

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

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.

Optimizing illumination in three-dimensional deconvolution microscopy for accurate refractive index tomography

In light transmission microscopy, axial scanning does not directly provide tomographic reconstruction of specimen. Phase deconvolution microscopy can convert a raw intensity image stack into a refractive index tomogram, the intrinsic sample contrast which can be exploited for quantitative morphological analysis. However, this technique is limited by reconstruction artifacts due to unoptimized optical conditions, which leads to a sparse and non-uniform optical transfer function. Here, we propose an optimization method based on simulated annealing to systematically obtain optimal illumination schemes that enable artifact-free deconvolution. The proposed method showed precise tomographic reconstruction of unlabeled biological samples.

Fabrication and Characterization of Human Serum Albumin Particles Loaded with Non-Sericin Extract Obtained from Silk Cocoon as a Carrier System for Hydrophobic Substances

Non-sericin (NS) extract was produced from the ethanolic extract of Bombyx mori silk cocoons. This extract is composed of both carotenoids and flavonoids. Many of these compounds are composed of substances of poor aqueous solubility. Thus, this study focused on the development of a carrier system created from biocompatible and biodegradable materials to improve the biological activity of NS extracts. Accordingly, NS was incorporated into human serum albumin template particles with MnCO₃ (NS-HSA MPs) by loading NS into the preformed HAS-MnCO₃ microparticles using the coprecipitation crosslinking dissolution technique (CCD-technique). After crosslinking and template dissolution steps, the NS loaded HSA particles are negatively charged, have a size ranging from 0.8 to 0.9 µm, and are peanut shaped. The degree of encapsulation efficiency ranged from 7% to 57% depending on the initial NS concentration and the steps of adsorption. In addition, NS-HSA MPs were taken up by human lung adenocarcinoma (A549 cell) for 24 h. The promotion of cellular uptake was evaluated by flow cytometry and the results produced 99% fluorescent stained cells. Moreover, the results from CLSM and 3D fluorescence imaging confirmed particle localization in the cells. Interestingly, NS-HSA MPs could not induce inflammation through nitric oxide production from macrophage RAW264.7 cells. This is the first study involving the loading of non-sericin extracts into HSA MPs by CCD technique to enhance the bioavailability and biological effects of NS. Therefore, HSA MPs could be utilized as a carrier system for hydrophobic substances targeting cells with albumin receptors.

Holotomography: Refractive Index as an Intrinsic Imaging Contrast for 3-D Label-Free Live Cell Imaging

Live cell imaging provides essential information in the investigation of cell biology and related pathophysiology. Refractive index (RI) can serve as intrinsic optical imaging contrast for 3-D label-free and quantitative live cell imaging, and provide invaluable information to understand various dynamics of cells and tissues for the study of numerous fields. Recently significant advances have been made in imaging methods and analysis approaches utilizing RI, which are now being transferred to biological and medical research fields, providing novel approaches to investigate the pathophysiology of cells. To provide insight into how RI can be used as an imaging contrast for imaging of biological specimens, here we provide the basic principle of RI-based imaging techniques and summarize recent progress on applications, ranging from microbiology, hematology, infectious diseases, hematology, and histopathology.

Deep-learning-based three-dimensional label-free tracking and analysis of immunological synapses of CAR-T cells

The immunological synapse (IS) is a cell-cell junction between a T cell and a professional antigen-presenting cell. Since the IS formation is a critical step for the initiation of an antigen-specific immune response, various live-cell imaging techniques, most of which rely on fluorescence microscopy, have been used to study the dynamics of IS. However, the inherent limitations associated with the fluorescence-based imaging, such as photo-bleaching and photo-toxicity, prevent the long-term assessment of dynamic changes of IS with high frequency. Here, we propose and experimentally validate a label-free, volumetric, and automated assessment method for IS dynamics using a combinational approach of optical diffraction tomography and deep learning-based segmentation. The proposed method enables an automatic and quantitative spatiotemporal analysis of IS kinetics of morphological and biochemical parameters associated with IS dynamics, providing a new option for immunological research.

Integrative quantitative-phase and airy light-sheet imaging

Light-sheet microscopy enables considerable speed and phototoxicity gains, while quantitative-phase imaging confers label-free recognition of cells and organelles, and quantifies their number-density that, thermodynamically, is more representative of metabolism than size. Here, we report the fusion of these two imaging modalities onto a standard inverted microscope that retains compatibility with microfluidics and open-source software for image acquisition and processing. An accelerating Airy-beam light-sheet critically enabled imaging areas that were greater by more than one order of magnitude than a Gaussian beam illumination and matched exactly those of quantitative-phase imaging. Using this integrative imaging system, we performed a demonstrative multivariate investigation of live-cells in microfluidics that unmasked that cellular noise can affect the compartmental localization of metabolic reactions. We detail the design, assembly, and performance of the integrative imaging system, and discuss potential applications in biotechnology and evolutionary biology.

Fast compressive lens-free tomography for 3D biological cell culture imaging

We present a compressive lens-free technique that performs tomographic imaging across a cubic millimeter-scale volume from highly sparse data. Compared with existing lens-free 3D microscopy systems, our method requires an order of magnitude fewer multi-angle illuminations for tomographic reconstruction, leading to a compact, cost-effective and scanning-free setup with a reduced data acquisition time to enable high-throughput 3D imaging of dynamic biological processes. We apply a fast proximal gradient algorithm with composite regularization to address the ill-posed tomographic inverse problem. Using simulated data, we show that the proposed method can achieve a reconstruction speed ∼10× faster than the state-of-the-art inverse problem approach in 3D lens-free microscopy. We experimentally validate the effectiveness of our method by imaging a resolution test chart and polystyrene beads, demonstrating its capability to resolve micron-size features in both lateral and axial directions. Furthermore, tomographic reconstruction results of neuronspheres and intestinal organoids reveal the potential of this 3D imaging technique for high-resolution and high-throughput biological applications.

3D morphological and biophysical changes in a single tachyzoite and its infected cells using three-dimensional quantitative phase imaging

Toxoplasma gondii is an apicomplexan parasite that causes toxoplasmosis in the human body and commonly infects warm-blooded organisms. Pathophysiology of its diseases is still an interesting issue to be studied since T gondii can infect nearly all nucleated cells. Imaging techniques are crucial for studying its pathophysiology. In T gondii-infected cells structural and biochemical alterations occurred. To study that modification, we use digital holotomography to investigate the structure and biochemical alteration of single tachyzoite and its infected cells in a label-free and quantitative manner. Quantification analysis was done by measuring the refractive index distribution, which provides information about the concentration and dry mass of individual cells. This study showed that holotomography could be effectively used to identify the structural and biochemical alteration in tremendously different cells in supporting pathophysiological research in particular for T gondii-caused diseases.

Label-Free Tomographic Imaging of Lipid Droplets in Foam Cells for Machine-Learning-Assisted Therapeutic Evaluation of Targeted Nanodrugs

Lipid droplet (LD) accumulation, a key feature of foam cells, constitutes an attractive target for therapeutic intervention in atherosclerosis. However, despite advances in cellular imaging techniques, current noninvasive and quantitative methods have limited application in living foam cells. Here, using optical diffraction tomography (ODT), we performed quantitative morphological and biophysical analysis of living foam cells in a label-free manner. We identified LDs in foam cells by verifying the specific refractive index using correlative imaging comprising ODT integrated with three-dimensional fluorescence imaging. Through time-lapse monitoring of three-dimensional dynamics of label-free living foam cells, we precisely and quantitatively evaluated the therapeutic effects of a nanodrug (mannose-polyethylene glycol-glycol chitosan-fluorescein isothiocyanate-lobeglitazone; MMR-Lobe) designed to affect the targeted delivery of lobeglitazone to foam cells based on high mannose receptor specificity. Furthermore, by exploiting machine-learning-based image analysis, we further demonstrated therapeutic evaluation at the single-cell level. These findings suggest that refractive index measurement is a promising tool to explore new drugs against LD-related metabolic diseases.

Real-time cholesterol sorting in Plasmodium falciparum-erythrocytes as revealed by 3D label-free imaging

Cholesterol, a necessary component of animal cell membranes, is also needed by the lethal human malaria parasite Plasmodium falciparum. Because P. falciparum lacks a cholesterol synthesis pathway and malaria patients have low blood cholesterol, we speculated that it scavenges cholesterol from them in some way. We used time-lapse holotomographic microscopy to observe cholesterol transport in live P. falciparum parasites and structurally investigate erythrocyte membranes, both during and after P. falciparum invasion of human erythrocytes. After P. falciparum initially acquired free cholesterol or inner erythrocytic membrane-derived cholesterol, we observed budding lipid membranes elongating into the cytosol and/or membrane segments migrating there and eventually fusing with the parasite membranes, presumably at the parasitophorous vacuole membrane (PVM). Finally, the cholesterol-containing segments were seen to surround the parasite nucleus. Our imaging data suggest that a novel membrane transport system operates in the cytosol of P. falciparum-infected erythrocytes as a cholesterol import system, likely between the PVM and the erythrocyte membrane, and that this transportation process occurs during the live erythrocyte stages of P. falciparum.

Super-resolution fluorescence-assisted diffraction computational tomography reveals the three-dimensional landscape of the cellular organelle interactome

The emergence of super-resolution (SR) fluorescence microscopy has rejuvenated the search for new cellular sub-structures. However, SR fluorescence microscopy achieves high contrast at the expense of a holistic view of the interacting partners and surrounding environment. Thus, we developed SR fluorescence-assisted diffraction computational tomography (SR-FACT), which combines label-free three-dimensional optical diffraction tomography (ODT) with two-dimensional fluorescence Hessian structured illumination microscopy. The ODT module is capable of resolving the mitochondria, lipid droplets, the nuclear membrane, chromosomes, the tubular endoplasmic reticulum, and lysosomes. Using dual-mode correlated live-cell imaging for a prolonged period of time, we observed novel subcellular structures named dark-vacuole bodies, the majority of which originate from densely populated perinuclear regions, and intensively interact with organelles such as the mitochondria and the nuclear membrane before ultimately collapsing into the plasma membrane. This work demonstrates the unique capabilities of SR-FACT, which suggests its wide applicability in cell biology in general.

Image-based analysis of living mammalian cells using label-free 3D refractive index maps reveals new organelle dynamics and dry mass flux

Holo-tomographic microscopy (HTM) is a label-free microscopy method reporting the fine changes of a cell's refractive indices (RIs) in three dimensions at high spatial and temporal resolution. By combining HTM with epifluorescence, we demonstrate that mammalian cellular organelles such as lipid droplets (LDs) and mitochondria show specific RI 3D patterns. To go further, we developed a computer-vision strategy using FIJI, CellProfiler3 (CP3), and custom code that allows us to use the fine images obtained by HTM in quantitative approaches. We could observe the shape and dry mass dynamics of LDs, endocytic structures, and entire cells' division that have so far, to the best of our knowledge, been out of reach. We finally took advantage of the capacity of HTM to capture the motion of many organelles at the same time to report a multiorganelle spinning phenomenon and study its dynamic properties using pattern matching and homography analysis. This work demonstrates that HTM gives access to an uncharted field of biological dynamics and describes a unique set of simple computer-vision strategies that can be broadly used to quantify HTM images.

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

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.

Versatile transmission/reflection tomographic diffractive microscopy approach

Tomographic diffractive microscopy (TDM) has gained interest in recent years due to its ability to deliver high-resolution, three-dimensional images of unlabeled samples. It has been applied to transparent samples in transmission mode, as well as to surface studies in reflection mode. Mudry et al. [Opt. Lett.35, 1857 (2010)OPLEDP0146-959210.1364/OL.35.001857] introduced the concept of mirror-assisted TDM (MA-TDM), an elegant approach for achieving quasi-isotropic-resolution microscopic imaging, but which is still to be experimentally applied. In this work, we show that a simplified version of MA-TDM allows for transforming a reflective TDM setup into a more versatile instrument, also capable of observing transparent samples in transmission mode if using specific sample holders made out of a mirror and coated with a low-thickness transparent spacer.