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Accelerating single molecule localization microscopy through parallel processing on a high-performance computing cluster
摘要： Super-resolved microscopy techniques have revolutionized the ability to study biological structures below the diffraction limit. Single molecule localization microscopy (SMLM) techniques are widely used because they are relatively straightforward to implement and can be realized at relatively low cost, e.g. compared to laser scanning microscopy techniques. However, while the data analysis can be readily undertaken using open source or other software tools, large SMLM data volumes and the complexity of the algorithms used often lead to long image data processing times that can hinder the iterative optimization of experiments. There is increasing interest in high throughput SMLM, but its further development and application is inhibited by the data processing challenges. We present here a widely applicable approach to accelerating SMLM data processing via a parallelized implementation of ThunderSTORM on a high-performance computing (HPC) cluster and quantify the speed advantage for a four-node cluster (with 24 cores and 128 GB RAM per node) compared to a high specification (28 cores, 128 GB RAM, SSD-enabled) desktop workstation. This data processing speed can be readily scaled by accessing more HPC resources. Our approach is not specific to ThunderSTORM and can be adapted for a wide range of SMLM software.
关键词： super-resolved microscopy,high-performance computing,Automated image analysis
更新于2025-11-21 11:24:58
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<i>In vivo</i> detection of endotracheal tube biofilms in intubated critical care patients using catheter-based optical coherence tomography
摘要： The formation of biofilms in the endotracheal tubes (ETTs) of intubated patients on mechanical ventilation is associated with a greater risk of ventilator-associated pneumonia (VAP) and death. New technologies are needed to detect and monitor ETTs in vivo for the presence of these biofilms. Longitudinal OCT imaging was performed in mechanically ventilated subjects at 24 hr intervals until extubation to detect the formation and temporal changes of in vivo ETT biofilms. OCT-derived attenuation coefficient images were used to differentiate between mucus and biofilm. Extubated ETTs were examined with optical and electron microscopy, and all imaging results were correlated with standard-of-care clinical test reports. OCT and attenuation coefficient images from 4 subjects were positive for ETT biofilms and were negative for 2 subjects. The processed and stained extubated ETTs and clinical reports confirmed the presence/absence of biofilms in all subjects. Our findings confirm that OCT can detect and differentiate between biofilm-positive and biofilm-negative groups (p < 10-5). OCT image-based features may serve as biomarkers for direct in vivo detection of ETT biofilms and help drive investigation of new management strategies to reduce the incidence of VAP.
关键词： attenuation coefficient image,endotracheal tube,biofilm,optical coherence tomography,ventilator-associated pneumonia
更新于2025-11-21 11:24:58
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Using Deep Learning with Large Dataset of Microscope Images to Develop an Automated Embryo Grading System
摘要： The assessment of embryo viability for in vitro fertilization (IVF) is mainly based on subjective visual analysis, with the limitation of intra- and inter-observer variation and a time-consuming task. In this study, we used deep learning with large dataset of microscopic embryo images to develop an automated grading system for embryo assessment. This study included a total of 171,239 images from 16,201 embryos of 4,146 IVF cycles at Stork Fertility Center (https://www.e-stork.com.tw) from March 6, 2014 to April 13, 2018. The images were captured by inverted microscope (Zeiss Axio Observer Z1) at 112 to 116 hours (Day 5) or 136 to 140 hours (Day 6) after fertilization. Using a pre-trained network trained on the ImageNet dataset as convolution base, we applied Convolutional Neural Network (CNN) on embryo images, using ResNet50 architecture to fine-tune ImageNet parameters. The predicted grading results was compared with the grading results from trained embryologists to evaluate the model performance. The images were labeled by trained embryologists, based on Gardner’s grading system: blastocyst development ranking from 3–6, ICM quality as A, B, or C; and TE quality as a, b, or c. After pre-processing, the images were divided into training, validation, and test groups, in which 60% were allocated to the training group, 20% to the validation group, and 20% to the test group. The ResNet50 algorithm was trained on the 60% images allocated to the training group, and the algorithm’s performance was evaluated using the 20% images allocated to the test group. The results showed an average predictive accuracy of 75.36% for the all three grading categories: 96.24% for blastocyst development, 91.07% for ICM quality, and 84.42% for TE quality. To the best of our knowledge, this is the first study of an automatic embryo grading system using large dataset from Asian population. Combing the promising results obtained in this study with time-lapse microscope system integrated with IVF Electronic Medical Record platform, a fully automated and non-invasive pipeline for embryo assessment will be achieved.
关键词： Embryo Grading,Machine Learning,Embryo Image,Artificial Intelligence
更新于2025-11-21 11:24:58
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Color Reproduction Accuracy Promotion of 3D-Printed Surfaces Based on Microscopic Image Analysis
摘要： Full-color 3D printing technology is a powerful process to manufacture intelligent customized colorful objects with improved surface qualities; however, poor surface color optimization methods are the main impeding factors for its commercialization. As such, the paper explored the correlation between microstructure and color reproduction, then an assessment and prediction method of color optimization based on microscopic image analysis was proposed. The experimental models were divided into 24-color plates and 4-color cubes printed by ProJet 860 3D printer, then impregnated according to preset parameters, at last measured by a spectrophotometer and observed using both a digital microscope and a scanning electron microscope. The results revealed that the samples manifested higher saturation and smaller chromatic aberration (ΔE) after post-processing. Moreover, the brightness of the same color surface increased with the increasing soaked surface roughness. Further, reduction in surface roughness, impregnation into surface pores, and enhancement of coating transparency effectively improved the accuracy of color reproduction, which could be verified by the measured values. Finally, the chromatic aberration caused by positioning errors on different faces of the samples was optimized, and the value of ΔE for a black cube was reduced from 8.12 to 0.82, which is undetectable to human eyes.
关键词： Structural characterisation,Impregnating process,Scanning electron microscope,Image analysis,Color optimization,Full-color printing
更新于2025-11-21 11:18:25
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A ratiometric fluorescence probe based on a novel recognition mechanism for monitoring endogenous hypochlorite in living cells
摘要： A ratiometric fluorescence probe (named ZOC) for the fast detection of HClO/ClO- was constructed by coumarin (donor) and pyridinium (acceptor) based on Forster resonance energy transfer (FRET) and intramolecular charge transfer (ICT) platform. ZOC possessed red emission signal (610 nm), large Stocks shift (190 nm), high energy transfer efficiency (95.3%), high selectivity and sensitivity, low detection limit (25 nM), wider detection range (from 25 nM to 30 μM), rapid response (within 13 S), and good biocompatibility. It was very interesting that the recognition mechanism involved a new organic reaction in which olefin double bond reacted first with HClO/ClO- regioselectively, followed by cyclization. ZOC was successfully used to the real time detection of endogenous HClO/ClO- in RAW 264.7 cells.
关键词： Hypochlorous acid/hypochlorite,Probe,Cell image,Ratiometric fluorescence,New mechanism
更新于2025-11-21 11:08:12
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In Vivo Fluorescence Retinal Imaging Following AAV2-Mediated Gene Delivery in the Rat Retina
摘要： PURPOSE. The purpose of this study was to evaluate longitudinal gene expression patterns by in vivo retinal imaging using a modified custom-built confocal laser-scanning microscope in experimental rats after intravitreal injection of recombinant adeno-associated virus 2 (rAAV2-green fluorescent protein [GFP]). METHODS. Ten 9-week-old Wistar rats were divided into two groups: experimental group (group 1) that received a rAAV2-GFP intravitreal injection and control group (group 2) that received a vehicle. After anesthesia using a Zoletil intraperitoneal injection, 8 μL rAAV2-GFP in group 1 or vehicle in group 2 was injected intravitreally using a 33-G Hamilton syringe. In vivo fluorescence retinal images were acquired under anesthesia at 2, 4, 6, and 13 days after rAAV or vehicle delivery. RESULTS. Differences in GFP fluorescence were identified starting from day 2 after the intravitreal injection of rAAV2-GFP in group 1. Between days 4 and 6, the intensity and area of fluorescence in the retina began to increase and peaked at day 13. Based on the pattern of GFP expression, the axon of the nerve fiber layer ganglion cell was identified. In group 2, eyes treated with the vehicle showed a small amount of autofluorescence in a limited area for up to 2 weeks, with no increase in intensity during this period. CONCLUSIONS. In vivo retinal imaging confirmed gene expression within 2 weeks after the intravitreal injection of rAAV2-GFP. Gene transfer and expression in the rat retina occurs quickly in 2 days and appears to peak within 2 weeks of gene delivery. In vivo retinal imaging may be a useful noninvasive tool to continuously monitor gene expression in the retina over time.
关键词： gene therapy,image analysis,retina
更新于2025-11-21 11:08:12
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A new FRET-based ratiometric fluorescence probe for hypochlorous acid and its imaging in living cells
摘要： A novel ratiometric fluorescence probe for hypochlorous acid was constructed by coumarin and pyridinium fluorophore based on the Forster resonance energy transfer (FRET) and intramolecular charge transfer (ICT) platform. In this ICT/FRET system, the energy transfer efficiency is high to 94.3%. Moreover, the probe could respond to hypochlorous acid with high selectivity and sensitivity, and exhibited a large Stokes shift. It was interesting to find that the probe could recognize hypochlorous acid via a new mechanism, in which the a -position of carbonyl group was oxidized to form a diketone derivative. More importantly, the probe was successfully applied to the ratiometric imaging of both exogenous and endogenous hypochlorous acid in living RAW 264.7 cells, with low toxicity and high photo-stability.
关键词： New reaction mechanism,FRET,Hypochlorous acid,Fluorescence probe,Cell image,Ratiometric
更新于2025-11-21 11:08:12
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[IEEE 2018 IEEE Global Conference on Signal and Information Processing (GlobalSIP) - Anaheim, CA, USA (2018.11.26-2018.11.29)] 2018 IEEE Global Conference on Signal and Information Processing (GlobalSIP) - DIGITAL STAINING OF HIGH-RESOLUTION FTIR SPECTROSCOPIC IMAGES
摘要： Histological stains, such as hemotaxylin and eosin (H&E), are commonly used to label tissue in clinical biopsies. However, these labels modify the tissue chemistry, making it difficult to use for further downstream analysis. Fourier transform infrared spectroscopy (FTIR) has shown promising results for characterizing disease-relevant tissues without chemical labels or dyes. However, tissue classification requires human annotation, which is difficult and tedious to acquire for complex samples. In addition, the results of a molecular analysis must be presented in a way that facilitates diagnosis for a trained pathologist. One proposed approach is digital staining, which uses machine learning to map an infrared spectroscopic image to the image that would be ideally produced with a chemical stain. While these methods produce promising results, the resolution is significantly lower than traditional histology. We demonstrate that high-resolution mappings can be obtained using FTIR imaging and histological staining of the same sample. In addition, we demonstrate that better results can be achieved with more recent convolutional neural networks (CNNs) that take advantage of both spatial and spectral features.
关键词： CNN,Digital staining,Image analysis,Histopathology
更新于2025-11-19 16:56:35
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High-performance flexible UV photodetectors based on AZO/ZnO/PVK/PEDOT:PSS heterostructures integrated on human hair
摘要： Flexible optoelectronics is an emerging research field that has attracted profound interest in recent years due to the special functions and potential applications of these devices in flexible image sensors, optical computing, energy conversion devices, Internet of Things and other technologies. Here, we demonstrate the high-performance UV photodetectors using AZO/ZnO nanorods/PVK/PEDOT:PSS heterostructures integrated on human hair. Due to the precise interfacial energy-level alignment among all layers and superior mechanical characteristics of human hair, the as-obtained photodetector shows a fast response time, high photoresponsivity and excellent flexibility. According to integrate 7 heterostructures as 7 display pixels, the flexible UV-image sensor has superior device performance and outstanding flexibility and can produce vivid and accurate images of Arabic numerals from 0 to 9. Different combinations of the two heterostructures can also be used to achieve flexible photon-triggered logic functions including AND, OR and NAND gates. The findings in this work indicate the possibility of using the human hair as fibre-shaped flexible substrate and will allow the use of hair-based hierarchical heterostructures as building blocks to create exciting opportunities for next generation high-performance, multifunctional, low-cost, and flexible optoelectronic devices.
关键词： photon-triggered logic gates,fast photoresponse,UV photodetectors,human hair,optical-image sensors
更新于2025-11-14 17:04:02
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Plastic anisotropy of laser melting deposited Ti–5Al–5Mo–5V–1Cr–1Fe titanium alloy
摘要： Tensile tests of laser melting deposited Ti–5Al–5Mo–5V–1Cr–1Fe titanium alloy specimens in different orientations were conducted, which indicates significant plastic anisotropy of this material. Digital image correlation method added in-situ-tensile tests were carried out to investigate mechanical properties with respect to specified material structures. The results indicate that the plasticity properties of the thick columnar grain and that of other grains are significant different. Under the same stress level, the thick columnar grain yield firstly and bear the main plastic deformation of the whole specimen. The elasto-plastic Poisson's ratio of the thick columnar grains and that of other grains are also different. Tests on layer bands indicate that the coarser microstructures of the layer bands lead a stronger resistance to tensile plastic deformation, but a weaker resistance to shear plastic deformation. In addition, the direction of primary α laths on both sides of the layer bands may be different, and this has an obviously effect on the tensile plastic deformation of the specimen.
关键词： Digital image correlation method,Plastic anisotropy,Laser melting deposited,Titanium alloy,Mechanical properties
更新于2025-10-24 16:40:20