Digital in-line holography for biological applications

Spatial incoherence-driven optical reconstruction of holograms with observer shift-invariance

Coherence preserves phase consistency between wavefields, enabling accurate recording and reconstruction in holography. Although recent advances in computational optics have realized holographic data acquisition using incoherent light by computationally retrieving information, optical reconstruction still requires partially coherent light sources. We demonstrate a hologram that reconstructs 3-dimensional distribution utilizing incoherence. By decomposing incoherent light into infinitesimal coherent lights and calculating their propagations, the incoherent sum is optimized to resemble the desired 3-dimensional scene, whereas individual coherent lights reconstruct completely different intensities. Incoherence provides high image quality and a wide eyebox, with the reconstructed intensity remaining shift-invariant under pupil displacement, allowing a 1000-fold expansion of the eyebox. We confirm the shift-invariance through a proof-of-concept experiment and demonstrate real-time synthesis of incoherent holograms using a neural network, significantly reducing computational costs. Our method could inspire new approaches in photonics using incoherent light and be practically adopted in holographic displays.

OAH-Net: a deep neural network for efficient and robust hologram reconstruction for off-axis digital holographic microscopy

Off-axis digital holographic microscopy is a high-throughput, label-free imaging technology that provides three-dimensional, high-resolution information about samples, which is particularly useful in large-scale cellular imaging. However, the hologram reconstruction process poses a significant bottleneck for timely data analysis. To address this challenge, we propose a novel reconstruction approach that integrates deep learning with the physical principles of off-axis holography. We initialized part of the network weights based on the physical principle and then fine-tuned them via supersized learning. Our off-axis hologram network (OAH-Net) retrieves phase and amplitude images with errors that fall within the measurement error range attributable to hardware, and its reconstruction speed significantly surpasses the microscope's acquisition rate. Crucially, OAH-Net, trained and validated on diluted whole blood samples, demonstrates remarkable external generalization capabilities on unseen samples with distinct patterns. Additionally, it can be seamlessly integrated with other models for downstream tasks, enabling end-to-end real-time hologram analysis. This capability further expands off-axis holography's applications in both biological and medical studies.

Non-contact lensless holographic reconstruction of diffractive intraocular lenses profiles

A lensless compact arrangement based on digital in-line holography under Gabor's regime is proposed as a novel contactless method to assess the profile of multifocal intraocular lenses (MIOLs) which are conformed by several diffractive rings. Diffractive MIOLs are a widely adopted ophthalmologic option for the correction of presbyopia in patients undergoing cataract surgery. The MIOL optical design might introduce non-negligible optical performance differences between lenses as well as the introduction of undesirable photic phenomena (such as halos and glare) affecting the vision of users. Therefore, the customized topographic control of each manufactured MIOL model, along with the advancement of optical simulation routines, is increasingly necessary to provide users with optimized performance of these implanted optics, as well as predictable and realistic expectations of their future vision with these solutions. In this manuscript, experimental results of the reconstruction of different smooth and highly edged diffractive profiles from a pair of commercially available MIOLs are presented. Besides, a study evaluating the convergence and robustness of the proposed iterative phase-retrieval routine based on a modified classical Gerchberg-Saxton algorithm is performed. These results provide experimental validation of the proposed technique for accurately measuring the optical profiles of MIOLs.

Simulation of digital lensless holographic microscopy holograms: a physics-image processing approach

This work presents a method for simulating digital lensless holographic microscopy (DLHM) holograms using a physics-based image processing approach. While DLHM has gained significant attention in biology, biomedicine, and environmental monitoring, the current modeling of DLHM holograms has been limited, hindering potential applications, including learning-based solutions and generative model training. In this study, the DLHM propagation process is decomposed into the diffraction of a complex-valued spherical wavefront and the non-homogeneous magnification of the diffracted field that encodes the sample information, which accelerates and enhances the hologram simulation. The proposed model is validated by comparing simulated and experimental holograms of standard test targets under diverse imaging conditions. Comparative analyses are conducted against other DLHM hologram modeling methods, including direct Rayleigh-Sommerfeld diffraction, its convolutional implementation, and the Fresnel-Bluestein formalism. The proposed model is shown to outperform these methods in overall similarity to experimental recordings across a wide range of imaging conditions while maintaining computational efficiency. This DLHM hologram modeling approach provides researchers with a powerful tool for simulating trustable holograms. The model can be publicly accessed through the open-access repository https://github.com/mloper23/DLHM-model.

Generalizable deep learning approach for 3D particle imaging using holographic microscopy (HM)

Despite its potential for label-free particle diagnostics, holographic microscopy is limited by specialized processing methods that struggle to generalize across diverse settings. We introduce a deep learning architecture leveraging human perception of longitudinal variation of diffracted patterns of particles, which enables highly generalizable analysis of 3D particle information with orders of magnitude improvement in processing speed. Trained with minimal synthetic and real holograms of simple particles, our method demonstrates exceptional performance across various challenging cases, including high particle concentrations, significant noise, and a wide range of particle sizes, complex shapes, and optical properties, exceeding the diversity of training datasets.

SLIM-assisted automatic cartography of cell death types and rates resulting from localized photodynamic treatment

We report a spatial light interference microscopy (SLIM)-based methodology aimed at automatic monitoring and analysis of changes in cellular morphology within extended fields of view in cytological samples. The experimental validation was performed on HeLa cells in vitro subjected to localized photodynamic treatment. The performed long-term noninvasive monitoring using the SLIM technique allowed us to estimate quantitative parameters characterizing the dynamics of average phase shift in individual cells and to reveal changes in their morphology specific for different mechanisms of cell death. The results obtained evidenced that the proposed SLIM-based methodology provides an opportunity for identification of cell death type and quantification of cell death rate in an automatic mode. The major sources of potential errors that can affect the results obtained are discussed. The developed methodology is promising for automatic monitoring of large ensembles of individual cells and for quantitative characterization of their response to various treatment modalities.

Quantitative phase imaging verification in large field-of-view lensless holographic microscopy via two-photon 3D printing

Large field-of-view (FOV) microscopic imaging (over 100 mm2) with high lateral resolution (1-2 μm) plays a pivotal role in biomedicine and biophotonics, especially within the label-free regime. Lensless digital holographic microscopy (LDHM) is promising in this context but ensuring accurate quantitative phase imaging (QPI) in large FOV LDHM is challenging. While phantoms, 3D printed by two-photon polymerization (TPP), have facilitated testing small FOV lens-based QPI systems, an equivalent evaluation for lensless techniques remains elusive, compounded by issues such as twin-image and beam distortions, particularly towards the detector's edges. Here, we propose an application of TPP over large area to examine phase consistency in LDHM. Our research involves fabricating widefield phase test targets with galvo and piezo scanning, scrutinizing them under single-shot twin-image corrupted conditions and multi-frame iterative twin-image minimization scenarios. By measuring the structures near the detector's edges, we verified LDHM phase imaging errors across the entire FOV, with less than 12% phase value difference between areas. Our findings indicate that TPP, followed by LDHM and Linnik interferometry cross-verification, requires new design considerations for precise large-area photonic manufacturing. This research paves the way for quantitative benchmarking of large FOV lensless phase imaging, enhancing understanding and further development of LDHM technique.

Use of a platform with lens-free shadow imaging technology to monitor natural killer cell activity

Natural killer (NK) cells are a crucial component of the innate immune system. This study introduces Cellytics NK, a novel platform for rapid and precise measurement of NK cell activity. This platform combines an NK-specific activation stimulator cocktail (ASC) and lens-free shadow imaging technology (LSIT), using optoelectronic components. LSIT captures digital hologram images of resting and ASC-activated NK cells, while an algorithm evaluates cell size and cytoplasmic complexity using shadow parameters. The combined shadow parameter derived from the peak-to-peak distance and width standard deviation rapidly distinguishes active NK cells from inactive NK cells at the single-cell level within 30 s. Here, the feasibility of the system was demonstrated by assessing NK cells from healthy donors and immunocompromised cancer patients, demonstrating a significant difference in the innate immunity index (I3). Cancer patients showed a lower I3 value (161%) than healthy donors (326%). I3 was strongly correlated with NK cell activity measured using various markers such as interferon-gamma, tumor necrosis factor-alpha, perforin, granzyme B, and CD107a. This technology holds promise for advancing immune functional assays, offering rapid and accurate on-site analysis of NK cells, a crucial innate immune cell, with its compact and cost-effective optoelectronic setup, especially in the post-COVID-19 era.

A customizable digital holographic microscope

We propose a compact, portable, and low-cost holographic microscope designed for the characterization of micrometric particles suspended in a liquid. This system is built around a commercial optical microscope by substituting its illumination source (a light-emitting diode) with a collimated laser beam. Similarly, a quartz flow cell replaces the microscope glass slide using a 3D-printed custom mount. With the hardware presented in this paper, the holographic imaging of the electromagnetic fields emitted by the particles that intercept the laser beam achieves a resolution close to that of optical microscopes but with a greater depth of field. Several morphological and optical features can be extracted from the holograms, including particle projected section, aspect ratio, and extinction cross-section. Additionally, we introduce a remote system control that enables users to process the acquired holograms on a remote computational device. This work provides a comprehensive description of the methodology of image processing in holographic microscopy and a series of validation measurements conducted using calibrated particles. This technique is suitable for the characterization of airborne particles found in snow, firn, and ice; here we report experimental results obtained from Alpine ice cores.

Roadmap on computational methods in optical imaging and holography [invited]

Computational methods have been established as cornerstones in optical imaging and holography in recent years. Every year, the dependence of optical imaging and holography on computational methods is increasing significantly to the extent that optical methods and components are being completely and efficiently replaced with computational methods at low cost. This roadmap reviews the current scenario in four major areas namely incoherent digital holography, quantitative phase imaging, imaging through scattering layers, and super-resolution imaging. In addition to registering the perspectives of the modern-day architects of the above research areas, the roadmap also reports some of the latest studies on the topic. Computational codes and pseudocodes are presented for computational methods in a plug-and-play fashion for readers to not only read and understand but also practice the latest algorithms with their data. We believe that this roadmap will be a valuable tool for analyzing the current trends in computational methods to predict and prepare the future of computational methods in optical imaging and holography.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00340-024-08280-3.

Digital in-line holographic microscopy for label-free identification and tracking of biological cells

Digital in-line holographic microscopy (DIHM) is a non-invasive, real-time, label-free technique that captures three-dimensional (3D) positional, orientational, and morphological information from digital holographic images of living biological cells. Unlike conventional microscopies, the DIHM technique enables precise measurements of dynamic behaviors exhibited by living cells within a 3D volume. This review outlines the fundamental principles and comprehensive digital image processing procedures employed in DIHM-based cell tracking methods. In addition, recent applications of DIHM technique for label-free identification and digital tracking of various motile biological cells, including human blood cells, spermatozoa, diseased cells, and unicellular microorganisms, are thoroughly examined. Leveraging artificial intelligence has significantly enhanced both the speed and accuracy of digital image processing for cell tracking and identification. The quantitative data on cell morphology and dynamics captured by DIHM can effectively elucidate the underlying mechanisms governing various microbial behaviors and contribute to the accumulation of diagnostic databases and the development of clinical treatments.

Off-axis digital lensless holographic microscopy based on spatially multiplexed interferometry

Significance

Digital holographic microscopy (DHM) is a label-free microscopy technique that provides time-resolved quantitative phase imaging (QPI) by measuring the optical path delay of light induced by transparent biological samples. DHM has been utilized for various biomedical applications, such as cancer research and sperm cell assessment, as well as for in vitro drug or toxicity testing. Its lensless version, digital lensless holographic microscopy (DLHM), is an emerging technology that offers size-reduced, lightweight, and cost-effective imaging systems. These features make DLHM applicable, for example, in limited resource laboratories, remote areas, and point-of-care applications.

Aim

In addition to the abovementioned advantages, in-line arrangements for DLHM also include the limitation of the twin-image presence, which can restrict accurate QPI. We therefore propose a compact lensless common-path interferometric off-axis approach that is capable of quantitative imaging of fast-moving biological specimens, such as living cells in flow.

Approach

We suggest lensless spatially multiplexed interferometric microscopy (LESSMIM) as a lens-free variant of the previously reported spatially multiplexed interferometric microscopy (SMIM) concept. LESSMIM comprises a common-path interferometric architecture that is based on a single diffraction grating to achieve digital off-axis holography. From a series of single-shot off-axis holograms, twin-image free and time-resolved QPI is achieved by commonly used methods for Fourier filtering-based reconstruction, aberration compensation, and numerical propagation.

Results

Initially, the LESSMIM concept is experimentally demonstrated by results from a resolution test chart and investigations on temporal stability. Then, the accuracy of QPI and capabilities for imaging of living adherent cell cultures is characterized. Finally, utilizing a microfluidic channel, the cytometry of suspended cells in flow is evaluated.

Conclusions

LESSMIM overcomes several limitations of in-line DLHM and provides fast time-resolved QPI in a compact optical arrangement. In summary, LESSMIM represents a promising technique with potential biomedical applications for fast imaging such as in imaging flow cytometry or sperm cell analysis.

Quantitative phase imaging techniques for measuring scattering properties of cells and tissues: a review-part I

Significance

Quantitative phase imaging (QPI) techniques offer intrinsic information about the sample of interest in a label-free, noninvasive manner and have an enormous potential for wide biomedical applications with negligible perturbations to the natural state of the sample in vitro.

Aim

We aim to present an in-depth review of the scattering formulation of light-matter interactions as applied to biological samples such as cells and tissues, discuss the relevant quantitative phase measurement techniques, and present a summary of various reported applications.

Approach

We start with scattering theory and scattering properties of biological samples followed by an exploration of various microscopy configurations for 2D QPI for measurement of structure and dynamics.

Results

We reviewed 157 publications and presented a range of QPI techniques and discussed suitable applications for each. We also presented the theoretical frameworks for phase reconstruction associated with the discussed techniques and highlighted their domains of validity.

Conclusions

We provide detailed theoretical as well as system-level information for a wide range of QPI techniques. Our study can serve as a guideline for new researchers looking for an exhaustive literature review of QPI methods and relevant applications.

Soft Contact Lens Engraving Characterization by Wavefront Holoscopy

Permanent engravings on contact lenses provide information about the manufacturing process and lens positioning when they are placed on the eye. The inspection of their morphological characteristics is important, since they can affect the user's comfort and deposit adhesion. Therefore, an inverted wavefront holoscope (a lensless microscope based on Gabor's principle of in-line digital holography) is explored for the characterization of the permanent marks of soft contact lenses. The device, based on an in-line transmission configuration, uses a partially coherent laser source to illuminate the soft contact lens placed in a cuvette filled with a saline solution for lens preservation. Holograms were recorded on a digital sensor and reconstructed by back propagation to the image plane based on the angular spectrum method. In addition, a phase-retrieval algorithm was used to enhance the quality of the recovered images. The instrument was experimentally validated through a calibration process in terms of spatial resolution and thickness estimation, showing values that perfectly agree with those that were theoretically expected. Finally, phase maps of different engravings for three commercial soft contact lenses were successfully reconstructed, validating the inverted wavefront holoscope as a potential instrument for the characterization of the permanent marks of soft contact lenses. To improve the final image quality of reconstructions, the geometry of lenses should be considered to avoid induced aberration effects.

Spatially-coded Fourier ptychography: flexible and detachable coded thin films for quantitative phase imaging with uniform phase transfer characteristics

Fourier ptychography (FP) is an enabling imaging technique that produces high-resolution complex-valued images with extended field coverages. However, when FP images a phase object with any specific spatial frequency, the captured images contain only constant values, rendering the recovery of the corresponding linear phase ramp impossible. This challenge is not unique to FP but also affects other common microscopy techniques -- a rather counterintuitive outcome given their widespread use in phase imaging. The underlying issue originates from the non-uniform phase transfer characteristic inherent in microscope systems, which impedes the conversion of object wavefields into discernible intensity variations. To address this challenge, we present spatially-coded Fourier ptychography (scFP), a new method that synergizes FP with spatial-domain coded detection for true quantitative phase imaging. In scFP, a flexible and detachable coded thin film is attached atop the image sensor in a regular FP setup. The spatial modulation of this thin film ensures a uniform phase response across the entire synthetic bandwidth. It improves reconstruction quality and corrects refractive index underestimation issues prevalent in conventional FP and related tomographic implementations. The inclusion of the coded thin film further adds a new dimension of measurement diversity in the spatial domain. The development of scFP is expected to catalyse new research directions and applications for phase imaging, emphasizing the need for true quantitative accuracy with uniform frequency response.

Physics-driven universal twin-image removal network for digital in-line holographic microscopy

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

Roadmap on Label-Free Super-Resolution Imaging

Label-free super-resolution (LFSR) imaging relies on light-scattering processes in nanoscale objects without a need for fluorescent (FL) staining required in super-resolved FL microscopy. The objectives of this Roadmap are to present a comprehensive vision of the developments, the state-of-the-art in this field, and to discuss the resolution boundaries and hurdles which need to be overcome to break the classical diffraction limit of the LFSR imaging. The scope of this Roadmap spans from the advanced interference detection techniques, where the diffraction-limited lateral resolution is combined with unsurpassed axial and temporal resolution, to techniques with true lateral super-resolution capability which are based on understanding resolution as an information science problem, on using novel structured illumination, near-field scanning, and nonlinear optics approaches, and on designing superlenses based on nanoplasmonics, metamaterials, transformation optics, and microsphere-assisted approaches. To this end, this Roadmap brings under the same umbrella researchers from the physics and biomedical optics communities in which such studies have often been developing separately. The ultimate intent of this paper is to create a vision for the current and future developments of LFSR imaging based on its physical mechanisms and to create a great opening for the series of articles in this field.

Investigating the Joint Amplitude and Phase Imaging of Stained Samples in Automatic Diagnosis

The diagnosis of many diseases relies, at least on first intention, on an analysis of blood smears acquired with a microscope. However, image quality is often insufficient for the automation of such processing. A promising improvement concerns the acquisition of enriched information on samples. In particular, Quantitative Phase Imaging (QPI) techniques, which allow the digitization of the phase in complement to the intensity, are attracting growing interest. Such imaging allows the exploration of transparent objects not visible in the intensity image using the phase image only. Another direction proposes using stained images to reveal some characteristics of the cells in the intensity image; in this case, the phase information is not exploited. In this paper, we question the interest of using the bi-modal information brought by intensity and phase in a QPI acquisition when the samples are stained. We consider the problem of detecting parasitized red blood cells for diagnosing malaria from stained blood smears using a Deep Neural Network (DNN). Fourier Ptychographic Microscopy (FPM) is used as the computational microscopy framework to produce QPI images. We show that the bi-modal information enhances the detection performance by 4% compared to the intensity image only when the convolution in the DNN is implemented through a complex-based formalism. This proves that the DNN can benefit from the bi-modal enhanced information. We conjecture that these results should extend to other applications processed through QPI acquisition.

Spatial- and Fourier-domain ptychography for high-throughput bio-imaging

First envisioned for determining crystalline structures, ptychography has become a useful imaging tool for microscopists. However, ptychography remains underused by biomedical researchers due to its limited resolution and throughput in the visible light regime. Recent developments of spatial- and Fourier-domain ptychography have successfully addressed these issues and now offer the potential for high-resolution, high-throughput optical imaging with minimal hardware modifications to existing microscopy setups, often providing an excellent trade-off between resolution and field of view inherent to conventional imaging systems, giving biomedical researchers the best of both worlds. Here, we provide extensive information to enable the implementation of ptychography by biomedical researchers in the visible light regime. We first discuss the intrinsic connections between spatial-domain coded ptychography and Fourier ptychography. A step-by-step guide then provides the user instructions for developing both systems with practical examples. In the spatial-domain implementation, we explain how a large-scale, high-performance blood-cell lens can be made at negligible expense. In the Fourier-domain implementation, we explain how adding a low-cost light source to a regular microscope can improve the resolution beyond the limit of the objective lens. The turnkey operation of these setups is suitable for use by professional research laboratories, as well as citizen scientists. Users with basic experience in optics and programming can build the setups within a week. The do-it-yourself nature of the setups also allows these procedures to be implemented in laboratory courses related to Fourier optics, biomedical instrumentation, digital image processing, robotics and capstone projects.

Image enhancement and field of view enlargement in digital lensless holographic microscopy by multi-shot imaging

A method to improve the quality of reconstructed images while the field of view (FOV) is enlarged in digital lensless holographic microscopy (DLHM) is presented. Multiple DLHM holograms are recorded while a still sample is located at different places of the plane containing it. The different locations of the sample must produce a set of DLHM holograms that share an overlapped area with a fixed DLHM hologram. The relative displacement among multiple DLHM holograms is computed by means of a normalized cross-correlation. The value of the computed displacement is utilized to produce a new DLHM hologram resulting from the coordinated addition of multi-shot DLHM holograms with the corresponding compensated displacement. The composed DLHM hologram carries enhanced information of the sample in a larger format, leading to a reconstructed image with improved quality and larger FOV. The feasibility of the method is illustrated and validated with results obtained from imaging a calibration test target and a biological specimen.

Single-shot wavelength-multiplexed phase microscopy under Gabor regime in a regular microscope embodiment

Phase imaging microscopy under Gabor regime has been recently reported as an extremely simple, low cost and compact way to update a standard bright-field microscope with coherent sensing capabilities. By inserting coherent illumination in the microscope embodiment and producing a small defocus distance of the sample at the input plane, the digital sensor records an in-line Gabor hologram of the target sample, which is then numerically post-processed to finally achieve the sample's quantitative phase information. However, the retrieved phase distribution is affected by the two well-known drawbacks when dealing with Gabor's regime, that is, coherent noise and twin image disturbances. Here, we present a single-shot technique based on wavelength multiplexing for mitigating these two effects. A multi-illumination laser source (including 3 diode lasers) illuminates the sample and a color digital sensor (conventional RGB color camera) is used to record the wavelength-multiplexed Gabor hologram in a single exposure. The technique is completed by presenting a novel algorithm based on a modified Gerchberg-Saxton kernel to finally retrieve an enhanced quantitative phase image of the sample, enhanced in terms of coherent noise removal and twin image minimization. Experimental validations are performed in a regular Olympus BX-60 upright microscope using a 20X 0.46NA objective lens and considering static (resolution test targets) and dynamic (living spermatozoa) phase samples.

DH-GAN: a physics-driven untrained generative adversarial network for holographic imaging

Digital holography is a 3D imaging technique by emitting a laser beam with a plane wavefront to an object and measuring the intensity of the diffracted waveform, called holograms. The object's 3D shape can be obtained by numerical analysis of the captured holograms and recovering the incurred phase. Recently, deep learning (DL) methods have been used for more accurate holographic processing. However, most supervised methods require large datasets to train the model, which is rarely available in most DH applications due to the scarcity of samples or privacy concerns. A few one-shot DL-based recovery methods exist with no reliance on large datasets of paired images. Still, most of these methods often neglect the underlying physics law that governs wave propagation. These methods offer a black-box operation, which is not explainable, generalizable, and transferrable to other samples and applications. In this work, we propose a new DL architecture based on generative adversarial networks that uses a discriminative network for realizing a semantic measure for reconstruction quality while using a generative network as a function approximator to model the inverse of hologram formation. We impose smoothness on the background part of the recovered image using a progressive masking module powered by simulated annealing to enhance the reconstruction quality. The proposed method exhibits high transferability to similar samples, which facilitates its fast deployment in time-sensitive applications without the need for retraining the network from scratch. The results show a considerable improvement to competitor methods in reconstruction quality (about 5 dB PSNR gain) and robustness to noise (about 50% reduction in PSNR vs noise increase rate).

Lens Free Holographic Imaging for Urinary Tract Infection Screening

OBJECTIVE

The diagnosis of urinary tract infection (UTI) currently requires precise specimen collection, handling infectious human waste, controlled urine storage, and timely transportation to modern laboratory equipment for analysis. Here we investigate holographic lens free imaging (LFI) to show its promise for enabling automatic urine analysis at the patient bedside.

METHODS

We introduce an LFI system capable of resolving important urine clinical biomarkers such as red blood cells, white blood cells, crystals, and casts in 2 mm thick urine phantoms.

RESULTS

This approach is sensitive to the particulate concentrations relevant for detecting several clinical urine abnormalities such as hematuria and pyuria, linearly correlating to ground truth hemacytometer measurements with R 2 = 0.9941 and R 2 = 0.9973, respectively. We show that LFI can estimate E. coli concentrations of 10 3 to 10 5 cells/mL by counting individual cells, and is sensitive to concentrations of 10 5 cells/mL to 10 8 cells/mL by analyzing hologram texture. Further, LFI measurements of blood cell concentrations are relatively insensitive to changes in bacteria concentrations of over seven orders of magnitude. Lastly, LFI reveals clear differences between UTI-positive and UTI-negative urine from human patients.

CONCLUSION

LFI is sensitive to clinically-relevant concentrations of bacteria, blood cells, and other sediment in large urine volumes.

SIGNIFICANCE

Together, these results show promise for LFI as a tool for urine screening, potentially offering early, point-of-care detection of UTI and other pathological processes.

Optical ptychography for biomedical imaging: recent progress and future directions [Invited]

Ptychography is an enabling microscopy technique for both fundamental and applied sciences. In the past decade, it has become an indispensable imaging tool in most X-ray synchrotrons and national laboratories worldwide. However, ptychography's limited resolution and throughput in the visible light regime have prevented its wide adoption in biomedical research. Recent developments in this technique have resolved these issues and offer turnkey solutions for high-throughput optical imaging with minimum hardware modifications. The demonstrated imaging throughput is now greater than that of a high-end whole slide scanner. In this review, we discuss the basic principle of ptychography and summarize the main milestones of its development. Different ptychographic implementations are categorized into four groups based on their lensless/lens-based configurations and coded-illumination/coded-detection operations. We also highlight the related biomedical applications, including digital pathology, drug screening, urinalysis, blood analysis, cytometric analysis, rare cell screening, cell culture monitoring, cell and tissue imaging in 2D and 3D, polarimetric analysis, among others. Ptychography for high-throughput optical imaging, currently in its early stages, will continue to improve in performance and expand in its applications. We conclude this review article by pointing out several directions for its future development.

Multi-Illumination Single-Holographic-Exposure Lensless Fresnel (MISHELF) Microscopy: Principles and Biomedical Applications

Lensless holographic microscopy (LHM) comes out as a promising label-free technique since it supplies high-quality imaging and adaptive magnification in a lens-free, compact and cost-effective way. Compact sizes and reduced prices of LHMs make them a perfect instrument for point-of-care diagnosis and increase their usability in limited-resource laboratories, remote areas, and poor countries. LHM can provide excellent intensity and phase imaging when the twin image is removed. In that sense, multi-illumination single-holographic-exposure lensless Fresnel (MISHELF) microscopy appears as a single-shot and phase-retrieved imaging technique employing multiple illumination/detection channels and a fast-iterative phase-retrieval algorithm. In this contribution, we review MISHELF microscopy through the description of the principles, the analysis of the performance, the presentation of the microscope prototypes and the inclusion of the main biomedical applications reported so far.

Experimental optimization of lensless digital holographic microscopy with rotating diffuser-based coherent noise reduction

Laser-based lensless digital holographic microscopy (LDHM) is often spoiled by considerable coherent noise factor. We propose a novel LDHM method with significantly limited coherent artifacts, e.g., speckle noise and parasitic interference fringes. It is achieved by incorporating a rotating diffuser, which introduces partial spatial coherence and preserves high temporal coherence of laser light, crucial for credible in-line hologram reconstruction. We present the first implementation of the classical rotating diffuser concept in LDHM, significantly increasing the signal-to-noise ratio while preserving the straightforwardness and compactness of the LDHM imaging device. Prior to the introduction of the rotating diffusor, we performed LDHM experimental hardware optimization employing 4 light sources, 4 cameras, and 3 different optical magnifications (camera-sample distances). It was guided by the quantitative assessment of numerical amplitude/phase reconstruction of test targets, conducted upon standard deviation calculation (noise factor quantification), and resolution evaluation (information throughput quantification). Optimized rotating diffuser LDHM (RD-LDHM) method was successfully corroborated in technical test target imaging and examination of challenging biomedical sample (60 µm thick mouse brain tissue slice). Physical minimization of coherent noise (up to 50%) was positively verified, while preserving optimal spatial resolution of phase and amplitude imaging. Coherent noise removal, ensured by proposed RD-LDHM method, is especially important in biomedical inference, as speckles can falsely imitate valid biological features. Combining this favorable outcome with large field-of-view imaging can promote the use of reported RD-LDHM technique in high-throughput stain-free biomedical screening.

Low-intensity illumination for lensless digital holographic microscopy with minimized sample interaction

Exposure to laser light alters cell culture examination via optical microscopic imaging techniques based on label-free coherent digital holography. To mitigate this detrimental feature, researchers tend to use a broader spectrum and lower intensity of illumination, which can decrease the quality of holographic imaging due to lower resolution and higher noise. We study the lensless digital holographic microscopy (LDHM) ability to operate in the low photon budget (LPB) regime to enable imaging of unimpaired live cells with minimized sample interaction. Low-cost off-the-shelf components are used, promoting the usability of such a straightforward approach. We show that recording data in the LPB regime (down to 7 µW of illumination power) does not limit the contrast or resolution of the hologram phase and amplitude reconstruction compared to regular illumination. The LPB generates hardware camera shot noise, however, to be effectively minimized via numerical denoising. The ability to obtain high-quality, high-resolution optical complex field reconstruction was confirmed using the USAF 1951 amplitude sample, phase resolution test target, and finally, live glial restricted progenitor cells (as a challenging strongly absorbing and scattering biomedical sample). The proposed approach based on severely limiting the photon budget in lensless holographic microscopy method can open new avenues in high-throughout (optimal resolution, large field-of-view, and high signal-to-noise-ratio single-hologram reconstruction) cell culture imaging with minimized sample interaction.

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.

Micro- and Nanoscale Imaging of Fluids in Water Using Refractive-Index-Matched Materials

Three-dimensional (3D) visualization in water is a technique that, in addition to macroscale visualization, enables micro- and nanoscale visualization via a microfabrication technique, which is particularly important in the study of biological systems. This review paper introduces micro- and nanoscale 3D fluid visualization methods. First, we introduce a specific holographic fluid measurement method that can visualize three-dimensional fluid phenomena; we introduce the basic principles and survey both the initial and latest related research. We also present a method of combining this technique with refractive-index-matched materials. Second, we outline the TIRF method, which is a method for nanoscale fluid measurements, and introduce measurement examples in combination with imprinted materials. In particular, refractive-index-matched materials are unaffected by diffraction at the nanoscale, but the key is to create nanoscale shapes. The two visualization methods reviewed here can also be used for other fluid measurements; however, because these methods can used in combination with refractive-index-matched materials in water, they are expected to be applied to experimental measurements of biological systems.

Accurate automatic object 4D tracking in digital in-line holographic microscopy based on computationally rendered dark fields

Building on Gabor seminal principle, digital in-line holographic microscopy provides efficient means for space-time investigations of large volumes of interest. Thus, it has a pivotal impact on particle tracking that is crucial in advancing various branches of science and technology, e.g., microfluidics and biophysical processes examination (cell motility, migration, interplay etc.). Well-established algorithms often rely on heavily regularized inverse problem modelling and encounter limitations in terms of tracking accuracy, hologram signal-to-noise ratio, accessible object volume, particle concentration and computational burden. This work demonstrates the DarkTrack algorithm-a new approach to versatile, fast, precise, and robust 4D holographic tracking based on deterministic computationally rendered high-contrast dark fields. Its unique capabilities are quantitatively corroborated employing a novel numerical engine for simulating Gabor holographic recording of time-variant volumes filled with predefined dynamic particles. Our solution accounts for multiple scattering and thus it is poised to secure an important gap in holographic particle tracking technology and allow for ground-truth-driven benchmarking and quantitative assessment of tracking algorithms. Proof-of-concept experimental evaluation of DarkTrack is presented via analyzing live spermatozoa. Software supporting both novel numerical holographic engine and DarkTrack algorithm is made open access, which opens new possibilities and sets the stage for democratization of robust holographic 4D particle examination.

Label-free single-shot imaging with on-axis phase-shifting holographic reflectance quantitative phase microscopy

Quantitative phase microscopy (QPM) has been emerged as an indispensable diagnostic and characterization tool in biomedical imaging with its characteristic nature of label-free, noninvasive, and real time imaging modality. The integration of holography to the conventional microscopy opens new advancements in QPM featuring high-resolution and quantitative three-dimensional image reconstruction. However, the holography schemes suffer in space-bandwidth and time-bandwidth issues in the off-axis and phase-shifting configuration, respectively. Here, we introduce an on-axis phase-shifting holography based QPM system with single-shot imaging capability. The technique utilizes the Fizeau interferometry scheme in combination with polarization phase-shifting and space-division multiplexing to achieve the single-shot recording of the multiple phase-shifted holograms. Moreover, the high-speed imaging capability with instantaneous recording of spatially phase shifted holograms offers the flexible utilization of the approach in dynamic quantitative phase imaging with robust phase stability. We experimentally demonstrated the validity of the approach by quantitative phase imaging and depth-resolved imaging of paramecium cells. Furthermore, the technique is applied to the phase imaging and quantitative parameter estimation of red blood cells. This integration of a Fizeau-based phase-shifting scheme to the optical microscopy enables a simple and robust tool for the investigations of engineered and biological specimen with real-time quantitative analysis.

Method for simultaneous tracking of thousands of unlabeled cells within a transparent 3D matrix

Three-dimensional tracking of cells is one of the most powerful methods to investigate multicellular phenomena, such as ontogenesis, tumor formation or wound healing. However, 3D tracking in a biological environment usually requires fluorescent labeling of the cells and elaborate equipment, such as automated light sheet or confocal microscopy. Here we present a simple method for 3D tracking large numbers of unlabeled cells in a collagen matrix. Using a small lensless imaging setup, consisting of an LED and a photo sensor only, we were able to simultaneously track ~3000 human neutrophil granulocytes in a collagen droplet within an unusually large field of view (>50 mm²) at a time resolution of 4 seconds and a spatial resolution of ~1.5 μm in xy- and ~30 μm in z-direction. The setup, which is small enough to fit into any conventional incubator, was used to investigate chemotaxis towards interleukin-8 (IL-8 or CXCL8) and N-formylmethionyl-leucyl-phenylalanine (fMLP). The influence of varying stiffness and pore size of the embedding collagen matrix could also be quantified. Furthermore, we demonstrate our setup to be capable of telling apart healthy neutrophils from those where a condition of inflammation was (I) induced by exposure to lipopolysaccharide (LPS) and (II) caused by a pre-existing asthma condition. Over the course of our experiments we have tracked more than 420.000 cells. The large cell numbers increase statistical relevance to not only quantify cellular behavior in research, but to make it suitable for future diagnostic applications, too.

Holographic point source for digital lensless holographic microscopy

A holographic point source (HPS) developed for digital lensless holographic microscopy (HPS-DLHM) is presented. The HPS is an off-axis phase transmission hologram of an experimental micrometer pinhole recorded on a photopolymer holographic film. An amplitude division interferometer, adjusted to operate at maximum diffraction efficiency, has been employed to record the hologram. The results of HPS-DLHM have been contrasted with the results obtained via conventional DLHM, and the two techniques were found to give similar measurements. Compared with conventional pinhole-based DLHM illumination, our cost-effective proposal provides increased mechanical stability, the possibility of wider spherical illumination cones, and shorter reconstruction distances. These superior features pave the way to applying this quantitative phase imaging (QPI) technique in biomedical and telemedicine applications. The imaging capabilities of our HPS-DLHM proposal have been tested by using an intricate sample of a honeybee leg, a low-absorption sample of epithelial cheek cells, a 1951 USAF test target, and smeared human erythrocytes.

An online flow-imaging particle counter and conventional water quality sensors detect drinking water contamination in the presence of normal water quality fluctuations

Contamination detection in drinking water is crucial for water utilities in terms of public health; however, current online water quality sensors can be unresponsive to various possible contaminants consisting of particulate and dissolved content or require a constant supply of reagents and sample preparation. We used a two-line test environment connected to a drinking water distribution system with flow-imaging particle counters and conventional sensors to assess their responses to the injection of contaminants into one line, including stormwater, treated wastewater, wastewater, well water, and Escherichia coli, while simultaneously measuring responses to normal water quality fluctuations in the other line. These water quality fluctuations were detected with all of the conventional sensors (except conductivity) and with 3 out of 5 of the size- and shape-derived particle classes of the flow-imaging particle counter. The flow-imaging particle counter was able to detect all of the studied contaminants, e.g. municipal wastewater at 0.001% (v/v), while the oxidation-reduction potential sensor outperformed other conventional sensors, detecting the same wastewater at 0.03% (v/v). The presence of particles less than 1 µm in size was shown to be a generic parameter for the detection of particulates present in the studied contaminants; however, they manifested a considerable response to fluctuations which led to lower relative response to contaminants in comparison to larger particles. The particle size and class distributions of contaminants were different from those of drinking water, and thus monitoring particles larger than 1 µm or specific particle classes of flow-imaging particle counter, which are substantially more abundant in contaminated water than in pure drinking water, can improve the detection of contamination events. Water utilities could optimize contamination detection by selecting water quality parameters with a minimal response to quality fluctuations and/or a high relative response to contaminants.

Single-Shot On-Axis Fizeau Polarization Phase-Shifting Digital Holography for Complex-Valued Dynamic Object Imaging

Digital holography assisted with inline phase-shifting methods has the benefit of a large field of view and a high resolution, but it is limited in dynamic imaging due to sequential detection of multiple holograms. Here we propose and experimentally demonstrate a single-shot phase-shifting digital holography system based on a highly stable on-axis Fizeau-type polarization interferometry. The compact on-axis design of the system with the capability of instantaneous recording of multiple phase-shifted holograms and with robust stability features makes the technique a novel tool for the imaging of complex-valued dynamic objects. The efficacy of the approach is demonstrated experimentally by complex field imaging of various kinds of reflecting-type static and dynamic objects. Moreover, a quantitative analysis on the robust phase stability and sensitivity of the technique is evaluated by comparing the approach with conventional phase-shifting methods. The high phase stability and dynamic imaging potential of the technique are expected to make the system an ideal tool for quantitative phase imaging and real-time imaging of dynamic samples.

Large depth-of-field fluorescence microscopy based on deep learning supported by Fresnel incoherent correlation holography

Fluorescence microscopy plays an irreplaceable role in biomedicine. However, limited depth of field (DoF) of fluorescence microscopy is always an obstacle of image quality, especially when the sample is with an uneven surface or distributed in different depths. In this manuscript, we combine deep learning with Fresnel incoherent correlation holography to describe a method to obtain significant large DoF fluorescence microscopy. Firstly, the hologram is restored by the Auto-ASP method from out-of-focus to in-focus in double-spherical wave Fresnel incoherent correlation holography. Then, we use a generative adversarial network to eliminate the artifacts introduced by Auto-ASP and output the high-quality image as a result. We use fluorescent beads, USAF target and mouse brain as samples to demonstrate the large DoF of more than 400µm, which is 13 times better than that of traditional wide-field microscopy. Moreover, our method is with a simple structure, which can be easily combined with many existing fluorescence microscopic imaging technology.

Kinematic analysis and visualization of Tetraselmis microalgae 3D motility by digital holography

A study on locomotion in a 3D environment of Tetraselmis microalgae by digital holographic microscopy is reported. In particular, a fast and semiautomatic criterion is revealed for tracking and analyzing the swimming path of a microalga (i.e., Tetraselmis species) in a 3D volume. Digital holography (DH) in a microscope off-axis configuration is exploited as a useful method to enable fast autofocusing and recognition of objects in the field of view, thus coupling DH with appropriate numerical algorithms. Through the proposed method we measure, simultaneously, the tri-dimensional paths followed by the flagellate microorganism and the full set of the kinematic parameters that describe the swimming behavior of the analyzed microorganisms by means of a polynomial fitting and segmentation. Furthermore, the method is capable to furnish the accurate morphology of the microorganisms at any instant of time along its 3D trajectory. This work launches a promising trend having as the main objective the combined use of DH and motility microorganism analysis as a label-free and non-invasive environmental monitoring tool, employable also for in situ measurements. Finally, we show that the locomotion can be visualized intriguingly by different modalities to furnish marine biologists with a clear 3D representation of all the parameters of the kinematic set in order to better understand the behavior of the microorganism under investigation.

Ptychographic sensor for large-scale lensless microbial monitoring with high spatiotemporal resolution

Traditional microbial detection methods often rely on the overall property of microbial cultures and cannot resolve individual growth event at high spatiotemporal resolution. As a result, they require bacteria to grow to confluence and then interpret the results. Here, we demonstrate the application of an integrated ptychographic sensor for lensless cytometric analysis of microbial cultures over a large scale and with high spatiotemporal resolution. The reported device can be placed within a regular incubator or used as a standalone incubating unit for long-term microbial monitoring. For longitudinal study where massive data are acquired at sequential time points, we report a new temporal-similarity constraint to increase the temporal resolution of ptychographic reconstruction by 7-fold. With this strategy, the reported device achieves a centimeter-scale field of view, a half-pitch spatial resolution of 488 nm, and a temporal resolution of 15-s intervals. For the first time, we report the direct observation of bacterial growth in a 15-s interval by tracking the phase wraps of the recovered images, with high phase sensitivity like that in interferometric measurements. We also characterize cell growth via longitudinal dry mass measurement and perform rapid bacterial detection at low concentrations. For drug-screening application, we demonstrate proof-of-concept antibiotic susceptibility testing and perform single-cell analysis of antibiotic-induced filamentation. The combination of high phase sensitivity, high spatiotemporal resolution, and large field of view is unique among existing microscopy techniques. As a quantitative and miniaturized platform, it can improve studies with microorganisms and other biospecimens at resource-limited settings.

Design, Calibration, and Application of a Robust, Cost-Effective, and High-Resolution Lensless Holographic Microscope

Lensless holographic microscope (LHM) is an emerging very promising technology that provides high-quality imaging and analysis of biological samples without utilizing any lens for imaging. Due to its small size and reduced price, LHM can be a very useful tool for the point-of-care diagnosis of diseases, sperm assessment, or microfluidics, among others, not only employed in advanced laboratories but also in poor and/or remote areas. Recently, several LHMs have been reported in the literature. However, complete characterization of their optical parameters remains not much presented yet. Hence, we present a complete analysis of the performance of a compact, reduced cost, and high-resolution LHM. In particular, optical parameters such as lateral and axial resolutions, lateral magnification, and field of view are discussed into detail, comparing the experimental results with the expected theoretical values for different layout configurations. We use high-resolution amplitude and phase test targets and several microbeads to characterize the proposed microscope. This characterization is used to define a balanced and matched setup showing a good compromise between the involved parameters. Finally, such a microscope is utilized for visualization of static, as well as dynamic biosamples.

Advancing the science of dynamic airborne nanosized particles using Nano-DIHM

In situ and real-time characterization of aerosols is vital to several fundamental and applied research domains including atmospheric chemistry, air quality monitoring, or climate change studies. To date, digital holographic microscopy is commonly used to characterize dynamic nanosized particles, but optical traps are required. In this study, a novel integrated digital in-line holographic microscope coupled with a flow tube (Nano-DIHM) is demonstrated to characterize particle phase, shape, morphology, 4D dynamic trajectories, and 3D dimensions of airborne particles ranging from the nanoscale to the microscale. We demonstrate the application of Nano-DIHM for nanosized particles (≤200 nm) in dynamic systems without optical traps. The Nano-DIHM allows observation of moving particles in 3D space and simultaneous measurement of each particle's three dimensions. As a proof of concept, we report the real-time observation of 100 nm and 200 nm particles, i.e. polystyrene latex spheres and the mixture of metal oxide nanoparticles, in air and aqueous/solid/heterogeneous phases in stationary and dynamic modes. Our observations are validated by high-resolution scanning/transmission electron microscopy and aerosol sizers. The complete automation of software (Octopus/Stingray) with Nano-DIHM permits the reconstruction of thousands of holograms within an hour with 62.5 millisecond time resolution for each hologram, allowing to explore the complex physical and chemical processes of aerosols.

Optofluidic ptychography on a chip

We report the implementation of a fully on-chip, lensless microscopy technique termed optofluidic ptychography. This imaging modality complements the miniaturization provided by microfluidics and allows the integration of ptychographic microscopy into various lab-on-a-chip devices. In our prototype, we place a microfluidic channel on the top surface of a coverslip and coat the bottom surface with a scattering layer. The channel and the coated coverslip substrate are then placed on top of an image sensor for diffraction data acquisition. Similar to the operation of a flow cytometer, the device utilizes microfluidic flow to deliver specimens across the channel. The diffracted light from the flowing objects is modulated by the scattering layer and recorded by the image sensor for ptychographic reconstruction, where high-resolution quantitative complex images are recovered from the diffraction measurements. By using an image sensor with a 1.85 μm pixel size, our device can resolve the 550 nm linewidth on the resolution target. We validate the device by imaging different types of biospecimens, including C. elegans, yeast cells, paramecium, and closterium sp. We also demonstrate a high-resolution ptychographic reconstruction at a video framerate of 30 frames per second. The reported technique can address a wide range of biomedical needs and engenders new ptychographic imaging innovations in a flow cytometer configuration.

Improving axial localization of weak phase particles in digital in-line holography

One shortcoming of digital in-line holography (DIH) is the low axial position accuracy due to the elongated particle traces in the reconstruction field. Here, we propose a method that improves the axial localization of DIH when applying it to track the motion of weak phase particles in dense suspensions. The proposed method detects particle positions based on local intensities in the reconstruction field consisting of scattering and incident waves. We perform both numerical and experimental tests and demonstrate that the proposed method has a higher axial position accuracy than the previous method based on the local intensities in the reconstructed scattered field. We show that the proposed method has an axial position error below 1.5 particle diameters for holograms with a particle concentration of 4700particles/mm³. The proposed method is further validated by tracking the Brownian motion of 1µmparticles in dense suspensions.

Plankton classification with high-throughput submersible holographic microscopy and transfer learning

BACKGROUND

Plankton are foundational to marine food webs and an important feature for characterizing ocean health. Recent developments in quantitative imaging devices provide in-flow high-throughput sampling from bulk volumes-opening new ecological challenges exploring microbial eukaryotic variation and diversity, alongside technical hurdles to automate classification from large datasets. However, a limited number of deployable imaging instruments have been coupled with the most prominent classification algorithms-effectively limiting the extraction of curated observations from field deployments. Holography offers relatively simple coherent microscopy designs with non-intrusive 3-D image information, and rapid frame rates that support data-driven plankton imaging tasks. Classification benchmarks across different domains have been set with transfer learning approaches, focused on repurposing pre-trained, state-of-the-art deep learning models as classifiers to learn new image features without protracted model training times. Combining the data production of holography, digital image processing, and computer vision could improve in-situ monitoring of plankton communities and contribute to sampling the diversity of microbial eukaryotes.

RESULTS

Here we use a light and portable digital in-line holographic microscope (The HoloSea) with maximum optical resolution of 1.5 μm, intensity-based object detection through a volume, and four different pre-trained convolutional neural networks to classify > 3800 micro-mesoplankton (> 20 μm) images across 19 classes. The maximum classifier performance was quickly achieved for each convolutional neural network during training and reached F1-scores > 89%. Taking classification further, we show that off-the-shelf classifiers perform strongly across every decision threshold for ranking a majority of the plankton classes.

CONCLUSION

These results show compelling baselines for classifying holographic plankton images, both rare and plentiful, including several dinoflagellate and diatom groups. These results also support a broader potential for deployable holographic microscopes to sample diverse microbial eukaryotic communities, and its use for high-throughput plankton monitoring.

Three-dimensional volumetric monitoring of settling particulate matters on a leaf using digital in-line holographic microscopy

Plants are considered as a possible modality to reduce particulate matter (PM) particles from ambient air in an ecofriendly manner. A new precise monitoring technique that can explore interactions between individual PM particles and a leaf surface is necessary to understand the underlying mechanisms of PM removal of plant leaves. In this study, a digital in-line holographic microscopy (DIHM) was employed to experimentally investigate the settling motions of PM particles over the leaf surface. The in-plane positions and sizes of opaque PMs with irregular shapes were obtained from the projection images of numerically reconstructed holographic images. The depth positions of PMs were determined by using proper selection of an autofocusing criterion with automatic segmentation method. The edge of a hairy Perilla frutescens leaf was detected by adopting several digital imaging processing techniques. The DIHM technique was applied in this study to accurately detect 3D settling trajectories of PMs with velocity information of PMs in the midair and near leaf surface, simultaneously.

Open-source, cost-effective, portable, 3D-printed digital lensless holographic microscope

In this work, the design, construction, and testing of the most cost-effective digital lensless holographic microscope to date are presented. The architecture of digital lensless holographic microscopy (DLHM) is built by means of a 3D-printed setup and utilizing off-the-shelf materials to produce a DLHM microscope costing US$52.82. For the processing of the recorded in-line holograms, an open-source software specifically developed to process this type of recordings is utilized. The presented DLHM setup has all the degrees of freedom needed to achieve different fields of view, levels of spatial resolution, and 2D scanning of the sample. The feasibility of the presented platform is tested by imaging non-bio and bio samples; the resolution test targets, a section of the head of a Drosophila melanogaster fly, red blood cells, and cheek cells are imaged on the built microscope.

Lensless digital holographic microscopy as an efficient method to monitor enzymatic plastic degradation

A big challenge of the 21st century is to cope with the huge amounts of plastic waste on Earth. Especially the oceans are heavily polluted with plastics. To counteract this issue, biological (enzymatic) plastic decomposition is increasingly gaining attention. Recently it was shown that polyethylene terephthalate (PET) can be degraded in a saltwater-based environment using bacterial PETase produced by a marine diatom. At moderate temperatures, plastic biodegradation is slow and requires sensitive methods for detection, at least at initial stages. However, conventional methods for verifying the plastic degradation are either complex, expensive, time-consuming or they interfere with the degradation process. Here, we adapt lensless digital holographic microscopy (LDHM) as a new application for efficiently monitoring enzymatic degradation of a PET glycol copolymer (PETG). LDHM is a cost-effective, compact and sensitive optical method. We demonstrate enzymatic PETG degradation over a time course of 43 days employing numerical analysis of LDHM images.

Digital plasmonic holography with iterative phase retrieval for sensing

Propagating surface plasmon waves have been used for many applications including imaging and sensing. However, direct in-plane imaging of micro-objects with surface plasmon waves suffers from the lack of simple, two-dimensional lenses, mirrors, and other optical elements. In this paper, we apply lensless digital holographic techniques and leakage radiation microscopy to achieve in-plane surface imaging with propagating surface plasmon waves. As plasmons propagate in two-dimensions and scatter from various objects, a hologram is formed over the surface. Iterative phase retrieval techniques applied to this hologram remove twin image interference for high-resolution in-plane imaging and enable further applications in real-time plasmonic phase sensing.

Preprocessing in digital lensless holographic microscopy for intensity reconstructions with enhanced contrast

In this work, a numerical method to enhance the contrast of intensity hologram reconstructions of digital lensless holographic microscopy (DLHM) is presented. The method manipulates the in-line hologram and reference images through mathematical operations between them; additionally, a sharpening operation, functionalized in terms of the parameters of the recording setup, is applied to the said images. The preprocessing of the recorded images produces a modified in-line hologram and a reference wave image from which an intensity reconstruction with a 25% improvement of its contrast, with respect to the conventional reconstruction procedure, is achieved. The method is illustrated with intensity reconstructions of a hologram of a monolayer of polystyrene spheres 1.09 µm in diameter. Finally, the preprocessing method is validated with a modeled hologram, successfully applied to holograms of the section of the head a Drosophila melanogaster fly and its results are contrasted with those obtained via bright-field microscopy.

High-Precision Lensless Microscope on a Chip Based on In-Line Holographic Imaging

The lensless on-chip microscope is an emerging technology in the recent decade that can realize the imaging and analysis of biological samples with a wide field-of-view without huge optical devices and any lenses. Because of its small size, low cost, and being easy to hold and operate, it can be used as an alternative tool for large microscopes in resource-poor or remote areas, which is of great significance for the diagnosis, treatment, and prevention of diseases. To improve the low-resolution characteristics of the existing lensless shadow imaging systems and to meet the high-resolution needs of point-of-care testing, here, we propose a high-precision on-chip microscope based on in-line holographic technology. We demonstrated the ability of the iterative phase recovery algorithm to recover sample information and evaluated it with image quality evaluation algorithms with or without reference. The results showed that the resolution of the holographic image after iterative phase recovery is 1.41 times that of traditional shadow imaging. Moreover, we used machine learning tools to identify and count the mixed samples of mouse ascites tumor cells and micro-particles that were iterative phase recovered. The results showed that the on-chip cell counter had high-precision counting characteristics as compared with manual counting of the microscope reference image. Therefore, the proposed high-precision lensless microscope on a chip based on in-line holographic imaging provides one promising solution for future point-of-care testing (POCT).

Measurement of Cell Volume Using In-Line Digital Holography

The measurement of the volume of blood cells is important for clinical diagnosis and patient management. While digital holography microscopy (DHM) has been used to obtain such information, previous off-axis setups usually involve a separated reference beam and are thus not very easy to implement. Here, we use the simple in-line Gabor setup without separation of a reference beam to measure the shape and volume of cells mounted on glass slides. Inherent to the in-line holograms, the reconstructed phase of the object is affected by the virtual image noise, producing errors in the cell volume measurement. We optimized our approach to use a single hologram without phase retrieval, increasing distance between cell and hologram plane to reduce the measurement error of cell volume to less than 6% in some instances. Therefore, the in-line Gabor setup can be a useful and simple tool to obtain volumetric and morphologic cellular information.