Low-magnification Objective Research Articles

Optical detection and enumeration of Escherichia coli and Salmonella enterica using a low-magnification light microscope

A rapid and cost-effective method for detecting bacterial cells from surfaces is critical to food safety, clinical hygiene, and pharmacy quality. Herein, we established an optical detection method based on a gold chip coating with 3-mercaptophenylboronic acid (3-MPBA) to capture bacterial cells, which allows for the detection and quantification of bacterial cells with a standard light microscope under low-magnification (10×) objective lens. Then, integrate the developed optical detection method with swab sampling to detect bacterial cells loading on stainless-steel surfaces. Using Salmonella enterica (SE1045) and Escherichia coli (E. coli OP50) as model bacterial cells, we achieved a capture efficiency of up to 76.0 ± 2.0 % for SE1045 cells and 81.1 ± 3.3 % for E. coli OP50 cells at 103 CFU/mL upon the optimized conditions, which slightly decreased with the increasing bacterial concentrations. Our assay showed good linear relationships between the concentrations of bacterial cells with the cell counting in images in the range of 103 -107 CFU/mL for SE1045, and 103 -108 CFU/mL for E. coli OP50 cells. The limit of detection (LOD) was 103 CFU/mL for both SE1045 and E. coli OP50 cells. A further increase in sensitivity in detecting E. coli OP50 cells was achieved through a heat treatment, enabling the LOD to be reduced as low as 102 CFU/mL. Furthermore, a preliminary application succeeded in assessing bacterial contamination on stainless-steel surfaces following integration with the approximately 40 % recovery rate, suggesting prospects for evaluating the bacteria from surfaces. The entire process was completed within around 2 h, costing merely a few dollars per sample. Considering the low cost of standard light microscopes, our method holds significant potential for practical industrial applications in bacterial contamination control on surfaces, especially in low-resource settings.

Full-Automatic High-Efficiency Mueller Matrix Microscopy Imaging for Tissue Microarray Inspection.

This paper proposes a full-automatic high-efficiency Mueller matrix microscopic imaging (MMMI) system based on the tissue microarray (TMA) for cancer inspection for the first time. By performing a polar decomposition on the sample's Mueller matrix (MM) obtained by a transmissive MMMI system we established, the linear phase retardance equivalent waveplate fast-axis azimuth and the linear phase retardance are obtained for distinguishing the cancerous tissues from the normal ones based on the differences in their polarization characteristics, where three analyses methods including statistical analysis, the gray-level co-occurrence matrix analysis (GLCM) and the Tamura image processing method (TIPM) are used. Previous MMMI medical diagnostics typically utilized discrete slices for inspection under a high-magnification objective (20×-50×) with a small field of view, while we use the TMA under a low-magnification objective (5×) with a large field of view. Experimental results indicate that MMMI based on TMA can effectively analyze the pathological variations in biological tissues, inspect cancerous cervical tissues, and thus contribute to the diagnosis of postoperative cancer biopsies. Such an inspection method, using a large number of samples within a TMA, is beneficial for obtaining consistent findings and good reproducibility.

Large-scale microscope with improved resolution using SRGAN

Due to the limited Space-Bandwidth Product (SBP) of optical microscopy system, the Numerical Aperture (NA) and Field of View (FOV)/ Depth of Field (DOF) of conventional optical microscopes are mutually restricted. In this paper, we propose a 20× large-scale (large FOV&DOF) microscope objective lens which is enhanced by deep neural network to achieve the improved resolution close to a 40× Olympus objective lens. Based on training a Super-resolution Generative Adversarial Network (SRGAN) model to transform low-resolution images into super-resolved ones, the resolution of input images captured by low magnification objective is greatly improved without any loss of FOV. And the network output images have better performance on DOF. We also compared SRGAN with two other deep-learning based methods to prove its superiority. Such large-scale microscope with improved resolution could serve to democratize super-resolution imaging.

Optogenetic Interrogation of Electrophysiological Dendritic Properties and Their Effect on Pacemaking Neurons from Acute Rodent Brain Slices.

Understanding dendritic excitability is essential for a complete and precise characterization of neurons' input-output relationships. Theoretical and experimental work demonstrates that the electrotonic and nonlinear properties of dendrites can alter the amplitude (e.g., through amplification) and latency of synaptic inputs as viewed in the axosomatic region where spike timing is determined. The gold-standard technique to study dendritic excitability is using dual-patch recordings with a high-resistance electrode used to patch a piece of distal dendrite in addition to a somatic patch electrode. However, this approach is often impractical when distal dendrites are too fine to patch. Therefore, we developed a technique that utilizes the expression of Channelrhodopsin-2 (ChR2) to study dendritic excitability in acute brain slices through the combination of a somatic patch electrode and optogenetic activation. The protocol describes how to prepare acute slices from mice that express ChR2 in specific cell types, and how to use two modes of light stimulation: proximal (which activates the soma and proximal dendrites in a ~100 µm diameter surrounding the soma) with the use of a high-magnification objective and full-field stimulation through a low-magnification objective (which activates the entire somato-dendritic field of the neuron). We use this technique in conjunction with various stimulation protocols to estimate model-based spectral components of dendritic filtering and the impact of dendrites on phase response curves, peri-stimulus time histograms, and entrainment of pacemaking neurons. This technique provides a novel use of optogenetics to study intrinsic dendritic excitability through the use of standard patch-clamp slice physiology. Key features • A method for studying the effects of electrotonic and nonlinear dendritic properties on the sub- and suprathreshold responses of pacemaking neurons. • Combines somatic patch clamp or perforated patch recordings with optogenetic activation in acute brain slices to investigate dendritic linear transformation without patching the dendrite. • Oscillatory illumination at various frequencies estimates spectral properties of the dendrite using subthreshold voltage-clamp recordings and studies entrainment of pacemakers in current clamp recordings. • This protocol uses Poisson white noise illumination to estimate dendritic phase response curves and peri-stimulus time histograms.

Low-cost 3D printed lenses for brightfield and fluorescence microscopy.

We present the fabrication and implementation of low-cost optical quality 3D printed lenses, and their application as microscope objectives with different prescriptions. The imaging performance of the 3D printed lenses was benchmarked against commercially available optics including a 20 mm focal length 12.7 mm diameter NBK-7 plano-convex lens used as a low magnification objective, and a separate high magnification objective featuring three 6 mm diameter NBK-7 lenses with different positive and negative focal lengths. We describe the design and manufacturing processes to produce high-quality 3D printed lenses. We tested their surface quality using a stylus profilometer, showing that they conform to that of commercial glass counterpart lenses. The 3D printed lenses were used as microscope objectives in both brightfield and epi-fluorescence imaging of specimens including onion, cyanobacteria, and variegated Hosta leaves, demonstrating a sub-cellular resolution performance obtained with low-cost 3D printed optical elements within brightfield and fluorescence microscopy.

Millimeter field-of-view miniature two-photon microscopy for brain imaging in freely moving mice.

Development of miniature two-photon microscopy (m2PM) has made it possible to observe fine structure and activity of neurons in the brain of freely moving animals. However, the imaging field-of-view of existing m2PM is still significantly smaller than that of miniature single-photon microscopy. Here we report that, through the design of low-magnification objective, large field-of-view scan lens and small tilt angle microscanner, a 2.5-g m2PM achieved a field-of-view of 1000 × 788 µm2, comparable to that of a typical single-photon miniscope. We demonstrated its capability by imaging neurons, dendrites and spines in the millimeter field-of-view, and simultaneous recording calcium activities, through a gradient-index lens, of approximately 400 neurons in the dorsal hippocampal CA1 in a freely moving mouse. Integrated with a detachable 1.2-g fast z-scanning module, it enables a 1000 × 788 × 500 µm3 volumetric neuronal imaging in the cerebral cortex. Thus, millimeter FOV m2PM provides a powerful tool for deciphering neuronal population dynamics in experimental paradigms allowing for animal's free movement.

Efficient Synthetic Aperture for Phaseless Fourier Ptychographic Microscopy with Hybrid Coherent and Incoherent Illumination (Laser Photonics Rev. 17(3)/2023)

Efficient Synthetic Aperture for Phaseless Fourier Ptychographic Microscopy In article number 2200201, Qian Chen, Chao Zuo, and co-workers introduce an efficient synthetic aperture for phaseless Fourier ptychographic microscopy (ESA-FPM), which employs both coherent and incoherent illuminations to maximize the efficiency of data and achieve high spatial-bandwidth product reconstruction with few acquisitions. Furthermore, a customized miniaturized ESA-FPM system with a high-numerical-aperture, low-magnification objective lens, and a high-brightness LED array is built, demonstrating its potential for biomedical and pathological applications.

Malaria Detection Accelerated: Combing a High-Throughput NanoZoomer Platform with a ParasiteMacro Algorithm.

Eradication of malaria, a mosquito-borne parasitic disease that hijacks human red blood cells, is a global priority. Microscopy remains the gold standard hallmark for diagnosis and estimation of parasitemia for malaria, to date. However, this approach is time-consuming and requires much expertise especially in malaria-endemic countries or in areas with low-density malaria infection. Thus, there is a need for accurate malaria diagnosis/parasitemia estimation with standardized, fast, and more reliable methods. To this end, we performed a proof-of-concept study using the automated imaging (NanoZoomer) platform to detect the malarial parasite in infected blood. The approach can be used as a steppingstone for malaria diagnosis and parasitemia estimation. Additionally, we created an algorithm (ParasiteMacro) compatible with free online imaging software (ImageJ) that can be used with low magnification objectives (e.g., 5×, 10×, and 20×) both in the NanoZoomer and routine microscope. The novel approach to estimate malarial parasitemia based on modern technologies compared to manual light microscopy demonstrated 100% sensitivity, 87% specificity, a 100% negative predictive value (NPV) and a 93% positive predictive value (PPV). The manual and automated malaria counts showed a good Pearson correlation for low- (R2 = 0.9377, r = 0.9683 and p < 0.0001) as well as high- parasitemia (R2 = 0.8170, r = 0.9044 and p < 0.0001) with low estimation errors. Our robust strategy that identifies and quantifies malaria can play a pivotal role in disease control strategies.

Synchronous measurement of surface deformation and gradient distribution in microstructures

In the traditional microfield speckle pattern interference measurement system, due to the use of high-magnification objective lens, the working distance is small and the shearing device cannot be introduced to implement shearography measurement. Thus the distribution of the deformation gradient on a microstructure surface cannot be measured. A system for the synchronous measurement of the surface deformation and gradient distribution of a microstructure was designed. Through the combination of focusing lens, convex lens, and low-magnification objective lens, the microstructure surface was clearly magnified and the internal distance of the system was enlarged. Thus the shearing device can be introduced to realize the shearography measurement under the microfield view. The synchronous full-field measurement of the structural surface deformation and its gradient distribution was further realized by the introduction of a reference light and designing of an optical path switch. In addition, the designed system had a zoom feature, which can facilitate the measurement in variable field of view in a certain range. The feasibility of the system was verified by theoretical analysis and experiment, and the practicability was validated by testing the chip and circuit board.

An apparatus for qualitative assessment of the shading ratio of oblique illumination and real-time high-contrast imaging.

Oblique illumination imaging can significantly improve the contrast of transparent thin samples. However, in traditional oblique illumination methods, either the condenser is offset or a block is added to the condenser, which makes it complicated and challenged to build a stable oblique illumination imaging. Herein, we present a method to measure the optimal shading ratio of oblique illumination in an inverted microscope, and develop an apparatus for stable high-speed high-contrast imaging with uniform brightness. At optimal shading ratio, the oblique illumination imaging has better imaging quality than differential interference contrast, which characteristic is independent on sample. In oblique illumination with low magnification objective, the images have uneven brightness. According to target brightness, we have developed a brightness unevenness correction algorithm to form uniform background brightness for oblique illumination. Integrating the algorithm with imaging acquisition, corrected oblique illumination microscopy is appropriate to observe living cells with high contrast.

Improved microscopy with ultraviolet surface excitation (MUSE) using high-index immersion illumination.

Microscopy with ultraviolet surface excitation (MUSE) typically has an optical sectioning thickness significantly larger than standard physical sectioning thickness, resulting in increased background fluorescence and higher feature density compared to formalin-fixed, paraffin-embedded physical sections. We demonstrate that high-index immersion with angled illumination significantly reduces optical sectioning thickness through increased angle of refraction of excitation light at the tissue interface. We present a novel objective dipping cap and waveguide-based MUSE illuminator design with high-index immersion and quantify the improvement in optical sectioning thickness, demonstrating an e-1 section thickness reduction to 6.67 µm in tissue. Simultaneously, the waveguide illuminator can be combined with high or low magnification objectives, and we demonstrate a 6 mm2 field of view, wider than a conventional 10x pathology objective. Finally, we show that resolution and contrast can be further improved using deconvolution and focal stacking, enabling imaging that is robust to irregular surface profiles on surgical specimens.

Influence of laser shape on thermal increase during micro‐Raman spectroscopy analyses

AbstractMicro‐Raman spectrometers are used in various domains, from archaeology to space exploration. These systems use microscope objectives to focus the laser onto the sample to be analysed. Although this method drastically increases the spatial resolution down to a few hundreds of nanometres, it is also commonly admitted that this focused laser beam may heat and alter the studied material. The setting of the laser power is thus a universal problem for any micro‐Raman spectroscopy user who has to find a compromise between the Raman signal intensity and the risk of thermal alteration. This parameter is not easy to set based on bibliographic references because, depending on the architecture of the system used, on the laser wavelength and on the sample, damage may occur at very different laser power levels. Here, we describe the different parameters that influence thermal increase induced by the laser and propose easy to make experiments to measure them. A series of experiments is then carried out to study the thermal alteration of various materials when exposed to a laser beam focused with the different microscope objectives of a micro‐Raman system. It is shown that, except for very thin samples or powdered materials, the relevant parameters to consider are the laser power at the sample surface and the duration of exposure to the laser beam, whatever the objective used. We also demonstrate that the risk of sample alteration is almost non‐existent for thick transparent materials. Interestingly, it is shown that, for semi‐transparent materials, alteration may occur at lower laser power for low magnification objectives than for high magnification objectives. These results are explained by the high aperture angle of microscope objectives which induces high dispersion of the laser within the sample.

Integration of polymeric membrane/dielectric sphere assemblies in microfluidic chips for enhanced-contrast imaging with low-magnification systems

Current microscopy systems for the imaging of microorganisms are expensive because of their optimized design toward resolution maximization and aberration correction. In situations where such an optimization is not needed, for instance to merely detect the presence of pathogens in liquids for on-site analyses, a potential approach is to use highly refractive spheres in combination with low-magnification objectives to increase the resolution and the sensitivity of the optical sensing system in a cost-effective fashion. Indeed, for point-of-need assays, integration of optical elements on a microfluidic device can bring several advantages, such as test parallelization/automation and low-volume consumption. We report a study on BaTiO3 spheres that are partially embedded in thin polymeric membranes of mismatched refractive index. We computed the transformation that the polymeric membrane/dielectric sphere assembly (PMDSA) mediates on the light originating from the sample toward the optical detector and shows its enhanced-detection potential for a low-magnification objective. We then propose a method to easily fabricate chips with custom designs and precise location of such dielectric spheres relative to the microfluidic structures for enhanced imaging of microorganisms. We applied this concept to the detection of living fluorescent bacteria, either flowing in aqueous medium or immobilized in hydrodynamic traps. We quantified the contrast gain provided by the PMDSA for short exposure when used with a low-magnification objective. By comparing with a high-magnification objective, we also show how longer-term imaging can be still reliably performed with a more cost-effective system. Since the present PMDSA concept combines the optical enhancement of low-magnification systems with the flexibility of microfluidic handling, it can be highly suitable for portable and cost-effective systems for on-site analysis, from flow cytometry to longer-term antibiotic testing.

Large field-of-view nanometer-sectioning microscopy by using metal-induced energy transfer and biexponential lifetime analysis

Total internal reflection fluorescence (TIRF) microscopy, which has about 100-nm axial excitation depth, is the method of choice for nanometer-sectioning imaging for decades. Lately, several new imaging techniques, such as variable angle TIRF microscopy, supercritical-angle fluorescence microscopy, and metal-induced energy transfer imaging, have been proposed to enhance the axial resolution of TIRF. However, all of these methods use high numerical aperture (NA) objectives, and measured images inevitably have small field-of-views (FOVs). Small-FOV can be a serious limitation when multiple cells need to be observed. We propose large-FOV nanometer-sectioning microscopy, which breaks the complementary relations between the depth of focus and axial sectioning by using MIET. Large-FOV imaging is achieved with a low-magnification objective, while nanometer-sectioning is realized utilizing metal-induced energy transfer and biexponential fluorescence lifetime analysis. The feasibility of our proposed method was demonstrated by imaging nanometer-scale distances between the basal membrane of human aortic endothelial cells and a substrate.

3D-Printed Bubble-Free Perfusion Cartridge System for Live-Cell Imaging.

The advent of 3D-printing technologies has had a significant effect on the development of medical and biological devices. Perfusion chambers are widely used for live-cell imaging in cell biology research; however, air-bubble invasion is a pervasive problem in perfusion systems. Although 3D printing allows the rapid fabrication of millifluidic and microfluidic devices with high resolution, little has been reported on 3D-printed fluidic devices with bubble trapping systems. Herein, we present a 3D-printed millifluidic cartridge system with bent and flat tapered flow channels for preventing air-bubble invasion, irrespective of bubble volume and without the need for additional bubble-removing devices. This system realizes bubble-free perfusion with a user-friendly interface and no-time-penalty manufacturing processes. We demonstrated the bubble removal capability of the cartridge by continually introducing air bubbles with different volumes during the calcium imaging of Sf21 cells expressing insect odorant receptors. Calcium imaging was conducted using a low-magnification objective lens to show the versatility of the cartridge for wide-area observation. We verified that the cartridge could be used as a chemical reaction chamber by conducting protein staining experiments. Our cartridge system is advantageous for a wide range of cell-based bioassays and bioanalytical studies, and can be easily integrated into portable biosensors.

Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage.

Site-specific DNA cleavage (SSDC) is a key step in many cellular processes, and it is crucial to gene editing. This work describes a kinetic assay capable of measuring SSDC in many single DNA molecules simultaneously. Bead-tethered substrate DNAs, each containing a single copy of the target sequence, are prepared in a microfluidic flow channel. An external magnet applies a weak force to the paramagnetic beads. The integrity of up to 1,000 individual DNAs can be monitored by visualizing the microbeads under darkfield imaging using a wide-field, low magnification objective. Injecting of a restriction endonuclease, NdeI, initiates the cleavage reaction. Video microscopy is used to record the exact moment of each DNA cleavage by observing the frame in which the associated bead moves up and out of the focal plane of the objective. Frame-by-frame bead counting quantifies the reaction, and an exponential fit determines the reaction rate. This method allows collection of quantitative and statistically significant data on single molecule SSDC reactions in a single experiment.

High-Throughput Deep Learning Microscopy Using Multi-Angle Super-Resolution

Biomedical applications such as pathology and hematology expect microscopes with high space-bandwidth product (SBP) which is difficult to achieve with conventional microscope setup. By applying a deep neural network, we demonstrate a high space-bandwidth product microscopic technique termed multi-angle super-resolution microscopy (MASRM) to achieve high-resolution imaging with the low-magnification objective. We design a multiple-branch deep residual network which extracts high-frequency information and color information in obliquely-illuminated low-resolution input images and generates high-resolution output. To train our network, we build a well-registered dataset in which both low-resolution input and high-resolution target are real captured images. We carry out detailed experiments to demonstrate the effectiveness of MASRM and compare it with a computational imaging technique termed Fourier ptychographic microscopy (FPM). This data-driven technique unleashes the potential of traditional microscopes with low cost and has broad prospects in biomedical applications.

Achieving extremely high optical contrast of atomically-thin MoS2

Extraordinarily high optical contrast is instrumental to research and applications of two-dimensional materials, such as, for rapid identification of thickness, characterisation of optical properties, and quality assessment. With optimal designs of substrate structures and light illumination conditions, unprecedented optical contrast of MoS2 on Au surfaces exceeding 430% for monolayer and over 2600% for bilayer is achieved. This is realised on custom-designed substrates of near-zero reflectance near the normal incidence. In particular, by using an aperture stop to restrict the angle of incidence, high-magnification objectives can be made to achieve extraordinarily high optical contrast in a similar way as the low-magnification objectives, but still retaining the high spatial resolution capability. The technique will allow small flakes of micrometre size to be located easily and identified with great accuracy, which will have significant implications in many applications.

Click chemistry-based amplification and detection of endogenous RNA and DNA molecules in situ using clampFISH probes.

Direct labeling and measurement of gene expression in single cells show the tremendous variability otherwise hidden in bulk measurements. Single-molecule RNA fluorescence in situ hybridization (FISH) has become a mainstay in laboratories worldwide for measuring gene expression with precision. However, this method remains relatively low throughput because the total fluorescent signal produced is weak and requires long exposure times and high magnification microscopy, which limits the total number of cells sampled in each image. As such, it is experimentally difficult and time-consuming to sample a large enough population of cells to visualize and quantify specific gene expression of rare cells directly. Several FISH-based tools were recently developed that retain single-molecule sensitivity and specificity while greatly amplifying the fluorescent signal, thus making FISH-based analysis possible using standard microscopes with low magnification objectives. These tools have also enabled the detection of smaller and more specific targets like splice junctions or single nucleotide polymorphisms. Here we will describe one such tool, clampFISH, an oligonucleotide-based fluorescence amplification strategy for visualizing genomic loci and individual RNA transcripts in fixed cells. ClampFISH maintains specificity while amplifying fluorescent signals, making it amenable to high throughput assays such as low magnification microscopy, spatial transcriptomics, and flow sorting. The clampFISH technique involves probing the target RNA or DNA using a series of C-shaped oligonucleotide probes, each with a 3' azide and a 5' alkyne. Hybridization of the probe with the target nucleic acid brings the azide and the alkyne in close proximity, allowing for ligation via bioorthogonal click chemistry (CuAAC). As a result, the probe forms a closed loop around the target sequence, thus enabling stringent washes to remove nonspecific binding in further rounds of amplification and retention of signal throughout liquid handling steps. Iterative rounds of hybridization with C-shaped, fluorescently labeled probes exponentially amplify the fluorescent signal. ClampFISH is simple to implement and expands the utility of in situ hybridization for multiple high throughput techniques such as low magnification microscopy, flow cytometry, and sorting based on RNA expression levels.

Digital refocusing and extended depth of field reconstruction in Fourier ptychographic microscopy.

Fourier ptychography microscopy (FPM) is a recently developed microscopic imaging method that allows the recovery of a high-resolution complex image by combining a sequence of bright and darkfield images acquired under inclined illumination. The capacity of FPM for high resolution imaging at low magnification makes it particularly attractive for applications in digital pathology which require imaging of large specimens such as tissue sections and blood films. To date most applications of FPM have been limited to imaging thin samples, simplifying both image reconstruction and analysis. In this work we show that, for samples of intermediate thickness (defined here as less than the depth of field of a raw captured image), numerical propagation of the reconstructed complex field allows effective digital refocusing of FPM images. The results are validated by comparison against images obtained with an equivalent high numerical aperture objective lens. We find that post reconstruction refocusing (PRR) yields images comparable in quality to adding a defocus term to the pupil function within the reconstruction algorithm, while reducing computing time by several orders of magnitude. We apply PRR to visualize FPM images of Giemsa-stained peripheral blood films and present a novel image processing pipeline to construct an effective extended depth of field image which optimally displays the 3D sample structure in a 2D image. We also show how digital refocusing allows effective correction of the chromatic focus shifts inherent to the low magnification objective lenses used in FPM setups, improving the overall quality of color FPM images.