Holographic tomography of the diatom Skeletonema pseudocostatum used as a bioindicator of heavy metal-polluted waters

Heavy metal contamination in aquatic environments poses a significant threat to microbial communities, yet the subcellular responses of phytoplankton to metal stress remain poorly understood. In particular, the effects of heavy metal exposure on the structural and physiological properties of diatoms require further investigation. Here, we analyze the impact of cadmium (Cd) and copper (Cu) exposure on the subcellular structures of the diatom Skeletonema pseudocostatum using holographic tomography. This imaging technique enables detailed visualization and quantitative analysis of diatom subcomponents, including frustules, protoplasm, vacuoles, and chloroplasts, under varying metal concentrations. The study aims to understand the changes in the mean refractive index (RI) and concentration (e.g., the ratio among cell dry mass and its biovolume) as indicators of cellular response to metal stress and to infer if such diatom can be used as sentinel species of heavy metal pollution. Findings indicate that diatoms exhibit significant variations in RI and internal cell density when exposed to different metal concentrations. Lower RI values observed at higher metal concentrations, can be considered as a sign of stress due to cytoplasm extrusion and/or vacuolization. The results highlight the potential of using S. pseudocostatum as a bioindicator for monitoring water metal pollution. Moreover, the results show that holographic tomography as useful tool for non-invasive, high-resolution cellular imaging of phytoplankton in environmental studies.

Moderate levels of dissolved iron stimulate cellular growth and increase lipid storage in Symbiodinium sp

Dinoflagellates in the family Symbiodiniaceae are fundamental in coral reef ecosystems and facilitate essential processes such as photosynthesis, nutrient cycling, and calcium carbonate production. Iron (Fe) is an essential element for the physiological processes of Symbiodiniaceae, yet its role remains poorly understood in the context of cellular development and metabolic health. Here, we investigated the effect of iron availability-0-100 nM Fe(III)-on Symbiodinium sp. ITS2 type A1 cultures and quantified cellular content using flow cytometry and holotomography. Moderate levels of dissolved Fe (50 nM) enhanced growth rates and cellular content development in Symbiodinium sp., including lipids and proteins. We observed distinct growth patterns, pigment concentrations, and cellular morphology under increasing Fe concentrations, indicating the influence of iron availability on cellular physiology. Nondestructive, label-free holotomographic microscopy enabled single-cell in vivo imaging, revealing higher intracellular lipid accumulation (+57%) in response to 50 nM Fe(III) enrichment. Our findings contribute to a deeper understanding of the relationship between iron availability and Symbiodinium sp. growth and cellular development, with potential implications for coral health and reef resilience in the face of environmental stressors.

Holotomography and atomic force microscopy: a powerful combination to enhance cancer, microbiology and nanotoxicology research

Modern imaging strategies are paramount to studying living systems such as cells, bacteria, and fungi and their response to pathogens, toxicants, and nanomaterials (NMs) as modulated by exposure and environmental factors. The need to understand the processes and mechanisms of damage, healing, and cell survivability of living systems continues to motivate the development of alternative imaging strategies. Of particular interest is the use of label-free techniques (microscopy procedures that do not require sample staining) that minimize interference of biological processes by foreign marking substances and reduce intense light exposure and potential photo-toxicity effects. This review focuses on the synergic capabilities of atomic force microscopy (AFM) as a well-developed and robust imaging strategy with demonstrated applications to unravel intimate details in biomedical applications, with the label-free, fast, and enduring Holotomographic Microscopy (HTM) strategy. HTM is a technique that combines holography and tomography using a low intensity continuous illumination laser to investigate (quantitatively and non-invasively) cells, microorganisms, and thin tissue by generating three-dimensional (3D) images and monitoring in real-time inner morphological changes. We first review the operating principles that form the basis for the complementary details provided by these techniques regarding the surface and internal information provided by HTM and AFM, which are essential and complimentary for the development of several biomedical areas studying the interaction mechanisms of NMs with living organisms. First, AFM can provide superb resolution on surface morphology and biomechanical characterization. Second, the quantitative phase capabilities of HTM enable superb modeling and quantification of the volume, surface area, protein content, and mass density of the main components of cells and microorganisms, including the morphology of cells in microbiological systems. These capabilities result from directly quantifying refractive index changes without requiring fluorescent markers or chemicals. As such, HTM is ideal for long-term monitoring of living organisms in conditions close to their natural settings. We present a case-based review of the principal uses of both techniques and their essential contributions to nanomedicine and nanotoxicology (study of the harmful effects of NMs in living organisms), emphasizing cancer and infectious disease control. The synergic impact of the sequential use of these complementary strategies provides a clear drive for adopting these techniques as interdependent fundamental tools.

Advanced Microscopy Techniques for Molecular Biophysics

Though microscopy is most often intended as a technique for providing qualitative assessment of cellular and subcellular properties, when coupled with other instruments such as wavelength selectors, lasers, photoelectric devices and computers, it can perform a wide variety of quantitative measurements, which are demanding in establishing relationships between the properties and structures of biological material in all their spatial and temporal complexities. These combinations of instruments are a powerful approach to improve non-destructive investigations of cellular and subcellular properties (both physical and chemical) at a macromolecular scale resolution. Since many subcellular compartments in living cells are characterized by structurally organized molecules, this review deals with three advanced microscopy techniques well-suited for these kind of investigations, i.e., microspectrophotometry (MSP), super-resolution localization microscopy (SRLM) and holotomographic microscopy (HTM). These techniques can achieve an insight view into the role intracellular molecular organizations such as photoreceptive and photosynthetic structures and lipid bodies play in many cellular processes as well as their biophysical properties. Microspectrophotometry uses a set-up based on the combination of a wide-field microscope and a polychromator, which allows the measurement of spectroscopic features such as absorption spectra. Super resolution localization microscopy combines dedicated optics and sophisticated software algorithms to overcome the diffraction limit of light and allow the visualization of subcellular structures and dynamics in greater detail with respect to conventional optical microscopy. Holotomographic microscopy combines holography and tomography techniques into a single microscopy set-up, and allows 3D reconstruction by means of the phase separation of biomolecule condensates. This review is organized in sections, which for each technique describe some general aspects, a peculiar theoretical aspect, a specific experimental configuration and examples of applications (fish and algae photoreceptors, single labeled proteins and endocellular aggregates of lipids).

Diel variations in the estimated refractive index of bulk oceanic particles

The index of refraction (n) of particles is an important parameter in optical models that aims to extract particle size and carbon concentrations from light scattering measurements. An inadequate choice of n can critically affect the characterization and interpretation of optically-derived parameters, including those from satellite-based models which provide the current view of how biogeochemical processes vary over the global ocean. Yet, little is known about how n varies over time and space to inform such models. Particularly, in situ estimates of n for bulk water samples and at diel-resolving time scales are rare. Here, we demonstrate a method to estimate n using simultaneously and independently collected particulate beam attenuation coefficients, particle size distribution data, and a Mie theory model. We apply this method to surface waters of the North Pacific Subtropical Gyre (NPSG) at hourly resolution. Clear diel cycles in n were observed, marked by minima around local sunrise and maxima around sunset, qualitatively consistent with several laboratory-based estimates of n for specific phytoplankton species. A sensitivity analysis showed that the daily oscillation in n amplitude was somewhat insensitive to broad variations in method assumptions, ranging from 11.3 ± 4.3% to 16.9 ± 2.9%. Such estimates are crucial for improvement of algorithms that extract the particle size and production from bulk optical measurements, and could potentially help establish a link between n variations and changes in cellular composition of in situ particles.

An Efficient Method of Observing Diatom Frustules via Digital Holographic Microscopy

Herein, we propose a convenient method to enable pretreatment of target objects using digital holographic microscopy (DHM). As a test sample, we used diatom frustules (Nitzschia sp.) as the target objects. In the generally used sample preparation method, the frustule suspension is added dropwise onto a glass substrate or into a glass chamber. While our work confirms good observation of purified frustules using the typical sample preparation method, we also demonstrate a new procedure to observe unseparated structures of frustules prepared by baking them on a mica surface. The baked frustules on the mica surface were transferred to a glass chamber with 1% sodium dodecyl sulfate solution. In this manner, the unseparated structures of the diatom frustules were clearly observed. Furthermore, metal-coated frustules prepared by sputtering onto them on a mica surface were also clearly observed using the same procedure. Our method can be applied for the observation of any target object that is pretreated on a solid surface. We expect our proposed method to be a basis for establishing DHM techniques for microscopic observations of biomaterials.

Towards machine learning for heterogeneous inverse scattering in 3D microscopy

Light propagating through a nonuniform medium scatters as it interacts with particles with different refractive properties such as cells in the tissue. In this work we aim to utilize this scattering process to learn a volumetric reconstruction of scattering parameters, in particular particle densities. We target microscopy applications where coherent speckle effects are an integral part of the imaging process. We argue that the key for successful learning is modeling realistic speckles in the training process. To this end, we build on the development of recent physically accurate speckle simulators. We also explore how to incorporate speckle statistics, such as the memory effect, in the learning framework. Overall, this paper contributes an analysis of multiple aspects of the network design including the learning architecture, the training data and the desired input features. We hope this study will pave the road for future design of learning based imaging systems in this challenging domain.

Plankton reconstruction through robust statistical optical tomography

Plankton interact with the environment according to their size and three-dimensional (3D) structure. To study them outdoors, these translucent specimens are imaged in situ. Light projects through a specimen in each image. The specimen has a random scale, drawn from the population's size distribution and random unknown pose. The specimen appears only once before drifting away. We achieve 3D tomography using such a random ensemble to statistically estimate an average volumetric distribution of the plankton type and specimen size. To counter errors due to non-rigid deformations, we weight the data, drawing from advanced models developed for cryo-electron microscopy. The weights convey the confidence in the quality of each datum. This confidence relies on a statistical error model. We demonstrate the approach on live plankton using an underwater field microscope.

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.

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.

High-resolution 3D refractive index microscopy of multiple-scattering samples from intensity images

Optical diffraction tomography (ODT) reconstructs a sample's volumetric refractive index (RI) to create high-contrast, quantitative 3D visualizations of biological samples. However, standard implementations of ODT use interferometric systems, and so are sensitive to phase instabilities, complex mechanical design, and coherent noise. Furthermore, their reconstruction framework is typically limited to weakly scattering samples, and thus excludes a whole class of multiple-scattering samples. Here, we implement a new 3D RI microscopy technique that utilizes a computational multi-slice beam propagation method to invert the optical scattering process and reconstruct high-resolution (NA > 1.0) 3D RI distributions of multiple-scattering samples. The method acquires intensity-only measurements from different illumination angles and then solves a nonlinear optimization problem to recover the sample's 3D RI distribution. We experimentally demonstrate the reconstruction of samples with varying amounts of multiple-scattering: a 3T3 fibroblast cell, a cluster of C. elegans embryos, and a whole C. elegans worm, with lateral and axial resolutions of ≤ 240 nm and ≤ 900 nm, respectively. The results of this work lays groundwork for future studies into using optical wavelengths to probe 3D RI distributions of highly scattering biological organisms.

Label-free non-invasive quantitative measurement of lipid contents in individual microalgal cells using refractive index tomography

Microalgae are promising candidates for biofuel production due to their high lipid content. To facilitate utilization of the microalgae for biofuel, rapid quantification of the lipid contents in microalgae is necessary. However, conventional methods based on the chemical extraction of lipids require a time-consuming destructive extraction process. Here, we demonstrate label-free, non-invasive, rapid quantification of the lipid contents in individual micro-algal cells measuring the three-dimensional refractive index tomograms. We measure three-dimensional refractive index distributions within Nannochloropsis oculata cells and find that lipid droplets are identifiable in tomograms by their high refractive index. In addition, we alter N. oculata under nitrogen deficiency by measuring the volume, lipid weight, and dry cell weight of individual cells. Characterization of individual cells allows correlative analysis between the lipid content and size of individual cells.

Tomographic phase microscopy: principles and applications in bioimaging [Invited]

Tomographic phase microscopy (TPM) is an emerging optical microscopic technique for bioimaging. TPM uses digital holographic measurements of complex scattered fields to reconstruct three-dimensional refractive index (RI) maps of cells with diffraction-limited resolution by solving inverse scattering problems. In this paper, we review the developments of TPM from the fundamental physics to its applications in bioimaging. We first provide a comprehensive description of the tomographic reconstruction physical models used in TPM. The RI map reconstruction algorithms and various regularization methods are discussed. Selected TPM applications for cellular imaging, particularly in hematology, are reviewed. Finally, we examine the limitations of current TPM systems, propose future solutions, and envision promising directions in biomedical research.

Three-dimensional label-free imaging and analysis of Pinus pollen grains using optical diffraction tomography

The structure of pollen grains is related to the reproductive function of the plants. Here, three-dimensional (3D) refractive index maps were obtained for individual conifer pollen grains using optical diffraction tomography (ODT). The 3D morphological features of pollen grains from pine trees were investigated using measured refractive index maps, in which distinct substructures were clearly distinguished and analyzed. Morphological and physiochemical parameters of the pollen grains were quantified from the obtained refractive index (RI) maps and used to quantitatively study the interspecific differences of pollen grains from different strains. Our results demonstrate that ODT can assess the structure of pollen grains. This label-free and rapid 3D imaging approach may provide a new platform for understanding the physiology of pollen grains.

Melittin-induced alterations in morphology and deformability of human red blood cells using quantitative phase imaging techniques

Here, the actions of melittin, the active molecule of apitoxin or bee venom, were investigated on human red blood cells (RBCs) using quantitative phase imaging techniques. High-resolution real-time 3-D refractive index (RI) measurements and dynamic 2-D phase images of individual melittin-bound RBCs enabled in-depth examination of melittin-induced biophysical alterations of the cells. From the measurements, morphological, intracellular, and mechanical alterations of the RBCs were analyzed quantitatively. Furthermore, leakage of haemoglobin (Hb) inside the RBCs at high melittin concentration was also investigated.

Identification of non-activated lymphocytes using three-dimensional refractive index tomography and machine learning

Identification of lymphocyte cell types are crucial for understanding their pathophysiological roles in human diseases. Current methods for discriminating lymphocyte cell types primarily rely on labelling techniques with magnetic beads or fluorescence agents, which take time and have costs for sample preparation and may also have a potential risk of altering cellular functions. Here, we present the identification of non-activated lymphocyte cell types at the single-cell level using refractive index (RI) tomography and machine learning. From the measurements of three-dimensional RI maps of individual lymphocytes, the morphological and biochemical properties of the cells are quantitatively retrieved. To construct cell type classification models, various statistical classification algorithms are compared, and the k-NN (k = 4) algorithm was selected. The algorithm combines multiple quantitative characteristics of the lymphocyte to construct the cell type classifiers. After optimizing the feature sets via cross-validation, the trained classifiers enable identification of three lymphocyte cell types (B, CD4+ T, and CD8+ T cells) with high sensitivity and specificity. The present method, which combines RI tomography and machine learning for the first time to our knowledge, could be a versatile tool for investigating the pathophysiological roles of lymphocytes in various diseases including cancers, autoimmune diseases, and virus infections.

Label-free high-resolution 3-D imaging of gold nanoparticles inside live cells using optical diffraction tomography

Delivery of gold nanoparticles (GNPs) into live cells has high potentials, ranging from molecular-specific imaging, photodiagnostics, to photothermal therapy. However, studying the long-term dynamics of cells with GNPs using conventional fluorescence techniques suffers from phototoxicity and photobleaching. Here, we present a method for 3-D imaging of GNPs inside live cells exploiting refractive index (RI) as imaging contrast. Employing optical diffraction tomography, 3-D RI tomograms of live cells with GNPs are precisely measured for an extended period with sub-micrometer resolution. The locations and contents of GNPs in live cells are precisely addressed and quantified due to their distinctly high RI values, which was validated by confocal fluorescence imaging of fluorescent dye conjugated GNPs. In addition, we perform quantitative imaging analysis including the segmentations of GNPs in the cytosol, the volume distributions of aggregated GNPs, and the temporal evolution of GNPs contents in HeLa and 4T1 cells.

Measurements of morphological and biophysical alterations in individual neuron cells associated with early neurotoxic effects in Parkinson's disease

Parkinson's disease (PD) is a common neurodegenerative disease. However, therapeutic methods of PD are still limited due to complex pathophysiology in PD. Here, optical measurements of individual neurons from in vitro PD model using optical diffraction tomography (ODT) are presented. By measuring 3D refractive index distribution of neurons, morphological and biophysical alterations in in-vitro PD model are quantitatively investigated. It was found that neurons show apoptotic features in early PD progression. The present approach will open up new opportunities for quantitative investigation of the pathophysiology of various neurodegenerative diseases. © 2017 International Society for Advancement of Cytometry.

Hyperspectral optical diffraction tomography

Here, we present a novel microscopic technique for measuring wavelength-dependent three-dimensional (3-D) distributions of the refractive indices (RIs) of microscopic samples in the visible wavelengths. Employing 3-D quantitative phase microscopy techniques with a wavelength-swept source, 3-D RI tomograms were obtained in the range of 450 - 700 nm with a spectral resolution of a few nanometers. The capability of the technique was demonstrated by measuring the hyperspectral 3-D RI tomograms of polystyrene beads, human red blood cells, and hepatocytes. The results demonstrate the potential for label-free molecular specific 3-D tomography of biological samples.

Label-free characterization of white blood cells by measuring 3D refractive index maps

The characterization of white blood cells (WBCs) is crucial for blood analyses and disease diagnoses. However, current standard techniques rely on cell labeling, a process which imposes significant limitations. Here we present three-dimensional (3D) optical measurements and the label-free characterization of mouse WBCs using optical diffraction tomography. 3D refractive index (RI) tomograms of individual WBCs are constructed from multiple two-dimensional quantitative phase images of samples illuminated at various angles of incidence. Measurements of the 3D RI tomogram of WBCs enable the separation of heterogeneous populations of WBCs using quantitative morphological and biochemical information. Time-lapse tomographic measurements also provide the 3D trajectory of micrometer-sized beads ingested by WBCs. These results demonstrate that optical diffraction tomography can be a useful and versatile tool for the study of WBCs.

Three-dimensional refractive index tomograms and deformability of individual human red blood cells from cord blood of newborn infants and maternal blood

Red blood cells (RBCs) from the cord blood of newborn infants have distinctive functions in fetal and infant development. To systematically investigate the biophysical characteristics of individual cord RBCs in newborn infants, a comparative study was performed on RBCs from the cord blood of newborn infants and from adult mothers or nonpregnant women using optical holographic microtomography. Optical measurements of the distributions of the three-dimensional refractive indices and the dynamic membrane fluctuations of individual RBCs were used to investigate the morphological, biochemical, and mechanical properties of cord, maternal, and adult RBCs at the individual cell level. The volume and surface area of the cord RBCs were significantly larger than those of the RBCs from nonpregnant women, and the cord RBCs had more flattened shapes than that of the RBCs in adults. In addition, the hemoglobin (Hb) content in the cord RBCs from newborns was significantly higher. The Hb concentration in the cord RBCs was higher than that in the nonpregnant women or maternal RBCs, but they were within the physiological range of adults. Interestingly, the amplitudes of the dynamic membrane fluctuations in cord RBCs were comparable to those in nonpregnant women and maternal RBCs, suggesting that the deformability of cord RBCs is similar to that of healthy RBCs in adults.