Compact, cost-effective and field-portable microscope prototype based on MISHELF microscopy

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.

Adapting a Blu-ray optical pickup unit as a point source for digital lensless holographic microscopy

The adaptation of an off-the-shelf Blu-ray optical pickup unit (OPU) into a highly versatile point source for digital lensless holographic microscopy (DLHM) is presented. DLHM performance is mostly determined by the optical properties of the point source of spherical waves used for free-space magnification of the sample's diffraction pattern; in particular, its wavelength and numerical aperture define the achievable resolution, and its distance to the recording medium sets the magnification. Through a set of straightforward modifications, a commercial Blu-ray OPU can be transformed into a DLHM point source with three selectable wavelengths, a numerical aperture of up to 0.85, and integrated micro-displacements in both axial and transversal directions. The functionality of the OPU-based point source is then experimentally validated in the observation of micrometer-sized calibrated samples and biological specimens of common interest, showing the feasibility of obtaining sub-micrometer resolution and offering a versatile option for the development of new cost-effective and portable microscopy devices.

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.

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.

Projected refractive index framework for multi-wavelength phase retrieval

Multi-wavelength phase retrieval provides a competitive solution to lensless holographic imaging that features a low-cost, compact design and high data acquisition speed. However, the existence of phase wraps poses a unique challenge for iterative reconstruction, and the resulting algorithms often suffer from limited generalizability and increased computational complexity. Here, we propose a projected refractive index framework for multi-wavelength phase retrieval that directly recovers the amplitude and unwrapped phase of the object. General assumptions are linearized and integrated into the forward model. Based on an inverse problem formulation, physical constraints and sparsity priors are incorporated, which ensures imaging quality under noisy measurements. We experimentally demonstrate high-quality quantitative phase imaging on a lensless on-chip holographic imaging system using three color LEDs.

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.

Miniaturized optimal incident light angle-fitted dark field system for contrast-enhanced real-time monitoring of 2D/3D-projected cell motions

In the field of biology, dark field microscopy provides superior insight into cells and subcellular structures. However, most dark field microscopes are equipped with a dark field filter and a light source on a 2D-based specimen, so only a flat sample can be observed in a limited space. We propose a compact cell monitoring system with built-in dark field filter with an optimized incident angle of the light source to provide real-time cell imaging and spatial cell monitoring for long-term free from phototoxicity. 2D projection imaging was implemented using a modular condenser lens to acquire high-contrast images. This enabled the long-term monitoring of cells, and the real-time monitoring of cell division and death. This system was able to image, by 2D projection, cells on the surface thinly coated with multiwalled carbon nanotubes, as well as living cells that migrated along the surface of glass beads and hydrogel droplets with a diameter of about 160 μm. The optimal incident light angle-fitted dark field system combines high-contrast imaging sensitivity and high spatial resolution to even image cells on 3D surfaces.

i-scope: A Compact automated fluorescence microscope for cell counting applications in low resource settings

Fluorescence microscopy has widespread applications across biological sciences. It has been routinely used for cell counting, which provides a preliminary diagnostic test for many infectious diseases. Conventional fluorescence microscopes are bulky, expensive, time-intensive and laborious. They often require trained operators to acquire and analyze data. We report a compact automated digital fluorescence microscopy system, i-scope, for cell counting applications. The i-scope employs a total internal reflection fluorescence (TIRF) mode of sample illumination, along with a brightfield mode. It has a magnification of 30X, an optical resolution of ~0.2 µm/pixel and offers sample scanning over 20 mm x 20 mm. A custom-written program enables automated image acquisition and analysis, thereby enhancing ease of operation. It has a compact form-factor and has been developed into a standalone system with a processing unit, screen, and other accessories to offer a portable and economic point-of-care diagnostic solution in low-resource settings. We analysed the performance of the i-scope for milk somatic cell enumeration and benchmarked it against that of a conventional fluorescence microscope.

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.

Recent Advances in Lensless Imaging

Lensless imaging provides opportunities to design imaging systems free from the constraints imposed by traditional camera architectures. Thanks to advances in imaging hardware, fabrication techniques, and new algorithms, researchers have recently developed lensless imaging systems that are extremely compact, lightweight or able to image higher-dimensional quantities. Here we review these recent advances and describe the design principles and their effects that one should consider when developing and using lensless imaging systems.

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.

Computer-assisted sperm analysis (CASA) in veterinary science: A review

Computer-assisted sperm analysis (CASA) allows an assessment of sperm motion and morphology more accurately and objectively than by subjective evaluation. Although, CASA instruments have improved significantly during last 40 years especially in terms of software, image capture and computer settings, little has changed regarding processes for analyzing sperm motion attributes. The main problem is related to validation, consistency and optimization of equipment and procedures. Differences among CASA systems denote problems of objective analysis of results between different semen processing units. If validated, CASA systems can provide a great tool to objectively compare sperm motility and morphology. Sperm motility is one of the indicators most evaluated before and after cryopreservation vis-à-vis quality and fertilizing ability. Researchers have determined a possible relationship of CASA outputs with bull fertility in vivo; however, a clear association has not yet been confirmed. Most CASA measures depend upon concentration, sample volume, type of extender, duration of analysis and thawing temperature. For each attribute, CASA software should provide outputs based on a range rather than means or medians for transformed data. The current review describes development, validation requirements, limitations and future expansions associated with CASA technology.

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.

Portable deep learning singlet microscope

Having the least lenses, the significant feature of the singlet imaging system, helps the development of the portable and cost-effective microscopes. A novel method of monochromatic/color singlet microscopy, which is combined with only one aspheric lens and deep learning computational imaging technology, is proposed in this article. The designed singlet aspheric lens is an approximate linear signal system, which means modulation-transfer-function curves on all field-of-views (5 mm diagonally) are almost coincident with each other. The purpose of the designed linear signal system is to further improve the resolution of our microscope by using deep learning algorithm. As a proof of concept, we designed a singlet microscopy based on our method, which weighs only 400 g. The experimental data and results of the sample USAF-1951 target and bio-sample (the Equisetum-arvense Strobile L.S), prove that the performance of the proposed singlet microscope is competitive to a commercial microscope with the 4X/NA0.1 objective lens. We believe that our idea and method would guide to design more cost-effective and powerful singlet imaging system.

Assessments of sperm quality integrating morphology, swimming patterns, bioenergetics and cell signalling

Spermatozoa are diverse in form and function and these differences impact on their fertilizing capacity. Because of considerable inter-male and inter-species differences in sperm traits, assessments of sperm quality demand that we consider variations at different levels. We should thus pay attention not only to average values but also intra- and inter-sperm population variations and subpopulation structure. Sperm shape and size evolve in reponse to postcopulatory sexual selection. Assessments of morphological variation, with conventional microscopy or with computer-assisted systems, should bear this in mind. In rodents sperm head shape is asymmetric so it requires more complex tools, such as geometric morphometrics. Sperm function also evolves under postcopulatory sexual selection and this could be used as a basis to assess sperm performance. Sperm cells swim actively to overcome barriers in the female tract and develop a peculiar motility pattern in the final stages prior to and during fertilization. Both types of movement can be analyzed by computer-assisted microscopy systems. Sperm have high energetic demands for cell homeostasis, motility, and signalling. Bioenergetics can be analyzed by various means, including extracellular flux analyses to characterize glycolysis and mitochondrial respiration. Finally, cell signalling during capacitation has received much attention and can be assessed by microscopy (conventional or computer-assisted) or flow cytometry. Recent advances in image-flow cytometry affords analyses of high cell numbers with spatial localization of subcellular changes, which will have a big impact in the development of functional tests for the andrology clinic and in sperm preservation and use in artificial insemination.

3D-printable portable open-source platform for low-cost lens-less holographic cellular imaging

Digital holographic microscopy is an emerging, potentially low-cost alternative to conventional light microscopy for micro-object imaging on earth, underwater and in space. Immediate access to micron-scale objects however requires a well-balanced system design and sophisticated reconstruction algorithms, that are commercially available, however not accessible cost-efficiently. Here, we present an open-source implementation of a lens-less digital inline holographic microscope platform, based on off-the-shelf optical, electronic and mechanical components, costing less than $190. It employs a Blu-Ray semiconductor-laser-pickup or a light-emitting-diode, a pinhole, a 3D-printed housing consisting of 3 parts and a single-board portable computer and camera with an open-source implementation of the Fresnel-Kirchhoff routine. We demonstrate 1.55 μm spatial resolution by laser-pickup and 3.91 μm by the light-emitting-diode source. The housing and mechanical components are 3D printed. Both printer and reconstruction software source codes are open. The light-weight microscope allows to image label-free micro-spheres of 6.5 μm diameter, human red-blood-cells of about 8 μm diameter as well as fast-growing plant Nicotiana-tabacum-BY-2 suspension cells with 50 μm sizes. The imaging capability is validated by imaging-contrast quantification involving a standardized test target. The presented 3D-printable portable open-source platform represents a fully-open design, low-cost modular and versatile imaging-solution for use in high- and low-resource areas of the world.

An update on boar semen assessments by flow cytometry and CASA

In the quest for predicting fertility of an individual, enhancing semen handling, dilution and storage protocols, and understanding the impact of environment and, andrologists have changed their approaches to semen analysis. The technologies used today are fast developing and readily implemented in research. Semen is one of a few naturally occurring monocellular suspensions, so sperm function analysis by flow cytometry (FC) and utilization of fluorochromes is an ideal technique for high throughput, objective and accurate analysis. The complementary use of microscopical assessments by Computer-Assisted Semen Analysis (CASA), where sperm cell parameters can be objectively assessed is equally important. The objectivity and repeatability of these techniques have driven research on the function, identification of heterogeneity and fertility of the ejaculate. The wealth of knowledge obtained from the application of these powerful methods has changed our view of the spermatozoon. Although there is some application of these methods in the industry producing boar semen for artificial insemination (AI) and to eliminate sires of sub-standard semen quality, uptake of advanced methods is still slow. Instruments are becoming cheaper and technically more user friendly. Standardization of methodology and optimization of instrument settings is important for full implementation of these systems, including comparison between labs. This review provides an update on two technologies: flow cytometry and CASA for objective analysis of boar semen quality.

Taking connected mobile-health diagnostics of infectious diseases to the field

Mobile health, or 'mHealth', is the application of mobile devices, their components and related technologies to healthcare. It is already improving patients' access to treatment and advice. Now, in combination with internet-connected diagnostic devices, it offers novel ways to diagnose, track and control infectious diseases and to improve the efficiency of the health system. Here we examine the promise of these technologies and discuss the challenges in realizing their potential to increase patients' access to testing, aid in their treatment and improve the capability of public health authorities to monitor outbreaks, implement response strategies and assess the impact of interventions across the world.

Effect of counting chamber depth on the accuracy of lensless microscopy for the assessment of boar sperm motility

Sperm motility is one of the most significant parameters in the prediction of male fertility. Until now, both motility analysis using an optical microscope and computer-aided sperm analysis (CASA-Mot) entailed the use of counting chambers with a depth to 20 µm. Chamber depth significantly affects the intrinsic sperm movement, leading to an artificial motility pattern. For the first time, laser microscopy offers the possibility of avoiding this interference with sperm movement. The aims of the present study were to determine the different motility patterns observed in chambers with depths of 10, 20 and 100 µm using a new holographic approach and to compare the results obtained in the 20-µm chamber with those of the laser and optical CASA-Mot systems. The ISAS®3D-Track results showed that values for curvilinear velocity (VCL), straight line velocity, wobble and beat cross frequency were higher for the 100-µm chambers than for the 10- and 20-µm chambers. Only VCL showed a positive correlation between chambers. In addition, Bayesian analysis confirmed that the kinematic parameters observed with the 100-µm chamber were significantly different to those obtained using chambers with depths of 10 and 20 µm. When an optical analyser CASA-Mot system was used, all kinematic parameters, except VCL, were higher with ISAS®3D-Track, but were not relevant after Bayesian analysis. Finally, almost three different three-dimensional motility patterns were recognised. In conclusion, the use of the ISAS®3D-Track allows for the analysis of the natural three-dimensional pattern of sperm movement.

Resolution enhancement method for lensless in-line holographic microscope with spatially-extended light source

We propose a resolution enhancement method for lensless in-line holographic microscope (LIHM) with spatially-extended light source, where the resolution is normally deteriorated by the insufficient spatial coherence of the illumination. In our LIHM setup, a light-emitting diode (LED), which was a spatially-extended light source, directly illuminated the sample, and the in-line hologram were recorded by a CMOS imaging sensor located behind the sample. In our holographic reconstruction process, the in-line hologram was first deconvoled with a properly resized image of the LED illumination area, and then back-propagated with scalar diffraction formula to reconstruct the sample image. We studied the hologram forming process and showed that the additional deconvolution process besides normal scalar diffraction reconstruction in LIHM can effectively enhance the imaging resolution. The resolution enhancements capability was calibrated by numerical simulations and imaging experiments with the U.S. air force target as the sample. We also used our LIHM to image the wing of a green lacewing to further demonstrate the capability of our methods for practical imaging applications. Our methods provide a way for LIHM to achieve satisfactory resolution with less stringent requirement for spatial coherence of the source and could reduce the cost for compact imaging system.