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1.
Methods Mol Biol ; 2814: 29-44, 2024.
Article in English | MEDLINE | ID: mdl-38954195

ABSTRACT

Expansion microscopy (ExM) is a superresolution technique for fixed specimens that improves resolution of a given microscopy system approximately fourfold. The gain in resolution in ExM is not achieved by improvement of the resolution of the microscope itself but by isotropic expansion of the sample. To achieve this, the sample is cross-linked to an expandable gel matrix that swells approximately fourfold by incubation in water. We have applied the method to Dictyostelium amoebae and discuss the pros and cons of different labeling techniques in combination with pre- and post-expansion staining protocols.


Subject(s)
Dictyostelium , Microscopy/methods , Staining and Labeling/methods , Microscopy, Fluorescence/methods
2.
Opt Lett ; 49(13): 3794-3797, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38950270

ABSTRACT

Open-top light-sheet (OTLS) microscopy offers rapid 3D imaging of large optically cleared specimens. This enables nondestructive 3D pathology, which provides key advantages over conventional slide-based histology including comprehensive sampling without tissue sectioning/destruction and visualization of diagnostically important 3D structures. With 3D pathology, clinical specimens are often labeled with small-molecule stains that broadly target nucleic acids and proteins, mimicking conventional hematoxylin and eosin (H&E) dyes. Tight optical sectioning helps to minimize out-of-focus fluorescence for high-contrast imaging in these densely labeled tissues but has been challenging to achieve in OTLS systems due to trade-offs between optical sectioning and field of view. Here we present an OTLS microscope with voice-coil-based axial sweeping to circumvent this trade-off, achieving 2 µm axial resolution over a 750 × 375 µm field of view. We implement our design in a non-orthogonal dual-objective (NODO) architecture, which enables a 10-mm working distance with minimal sensitivity to refractive index mismatches, for high-contrast 3D imaging of clinical specimens.


Subject(s)
Imaging, Three-Dimensional , Imaging, Three-Dimensional/methods , Humans , Microscopy/methods , Staining and Labeling , Light
3.
BMC Infect Dis ; 24(1): 660, 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38956504

ABSTRACT

INTRODUCTION: Tuberculosis is a global health problem that causes 1. 4 million deaths every year. It has been estimated that sputum smear-negative diagnosis but culture-positive pulmonary TB diagnosis contribute to 12.6% of pulmonary TB transmission. TB diagnosis by smear microscopy smear has a minimum detection limit (LOD) of 5,000 to 10,000 bacilli per milliliter (CFU/ml) of sputum result in missed cases and false positives. However, GeneXpert technology, with a LOD of 131-250 CFU/ml in sputum samples and its implementation is believe to facilitate early detection TB and drug-resistant TB case. Since 2013, Ghana health Service (GHS) introduce GeneXpert MTB/RIF diagnostic in all regional hospitals in Ghana, however no assessment of performance between microscopy and GeneXpert TB diagnosis cross the health facilities has been reported. The study compared the results of routine diagnoses of TB by microscopy and Xpert MTB from 2016 to 2020 at the Cape Coast Teaching Hospital (CCTH). METHODS: The study compared routine microscopic and GeneXpert TB diagnosis results at the Cape Coast Teaching Hospital (CCTH) from 2016 to 2020 retrospectively. Briefly, sputum specimens were collected into 20 mL sterile screw-capped containers for each case of suspected TB infection and processed within 24 h. The samples were decontaminated using the NALC-NaOH method with the final NaOH concentration of 1%. The supernatants were discarded after the centrifuge and the remaining pellets dissolved in 1-1.5 ml of phosphate buffer saline (PBS) and used for diagnosis. A fixed smears were Ziehl-Neelsen acid-fast stain and observed under microscope and the remainings were used for GeneXpert MTB/RIF diagnosis. The data were analyze using GraphPad Prism. RESULTS: 50.11% (48.48-51.38%) were females with an odd ratio (95% CI) of 1.004 (0.944-1.069) more likely to report to the TB clinic for suspected TB diagnosis. The smear-positive cases for the first sputum were 6.6% (5.98-7.25%), and the second sputum was 6.07% (5.45-6.73%). The Xpert MTB-RIF diagnosis detected 2.93% (10/341) (1.42-5.33%) in the first and 5.44% (16/294) (3.14-8.69%) in the second smear-negative TB samples. The prevalence of Xpert MTB-RIF across smear positive showed that males had 56.87% (178/313) and 56.15% (137/244) and females had 43.13% (135/313) and 43.85% (107/244) for the first and second sputum. Also, false negative smears were 0.18% (10/5607) for smear 1 and 0.31% (16/5126) for smear 2. CONCLUSION: In conclusion, the study highlights the higher sensitivity of the GeneXpert assay compared to traditional smear microscopy for detecting MTB. The GeneXpert assay identified 10 and 16 positive MTB from smear 1 and smear 2 samples which were microscopic negative.


Subject(s)
Hospitals, Teaching , Microscopy , Mycobacterium tuberculosis , Sputum , Tuberculosis, Pulmonary , Humans , Mycobacterium tuberculosis/isolation & purification , Mycobacterium tuberculosis/genetics , Retrospective Studies , Sputum/microbiology , Ghana/epidemiology , Female , Adult , Male , Microscopy/methods , Middle Aged , Tuberculosis, Pulmonary/diagnosis , Tuberculosis, Pulmonary/microbiology , Young Adult , Adolescent , Sensitivity and Specificity , Aged , Molecular Diagnostic Techniques/methods , Child , Child, Preschool
4.
Brain Nerve ; 76(7): 807-812, 2024 Jul.
Article in Japanese | MEDLINE | ID: mdl-38970316

ABSTRACT

Two-photon excitation microscopy enables in vivo deep-tissue imaging within organisms. This technique is based on two-photon excitation, a nonlinear optical process that uses near-infrared light for excitation, resulting in high tissue permeability. Notably, two-photon excitation occurs only near the focal plane; therefore, minimally invasive tomographic images can be obtained. Owing to these features, two-photon excitation microscopy is currently widely used in medical and life-science research, particularly in the domain of neuroscience for in vivo visualization of deep tissues. However, the use of long-wavelength excitation light in two-photon excitation microscopy has resulted in a larger focused spot size and relatively low spatial resolution, which is a limitation of this technique for further applications. Recent studies have described super-resolution microscopy techniques applied to two-photon excitation microscopy in an attempt to observe living organisms "as they are in their natural state" with high spatial resolution. We have also addressed this topic using an optical approach (two-photon stimulated emission depletion microscopy) and an image analysis approach (two-photon super-resolution radial fluctuation). Here, we describe these approaches together with a discussion of our recent accomplishments.


Subject(s)
Microscopy, Fluorescence, Multiphoton , Animals , Humans , Microscopy, Fluorescence, Multiphoton/methods , Photons , Microscopy/methods , Image Processing, Computer-Assisted/methods
5.
Methods Enzymol ; 700: 217-234, 2024.
Article in English | MEDLINE | ID: mdl-38971601

ABSTRACT

Sphingomyelin is postulated to form clusters with glycosphingolipids, cholesterol and other sphingomyelin molecules in biomembranes through hydrophobic interaction and hydrogen bonds. These clusters form submicron size lipid domains. Proteins that selectively binds sphingomyelin and/or cholesterol are useful to visualize the lipid domains. Due to their small size, visualization of lipid domains requires advanced microscopy techniques in addition to lipid binding proteins. This Chapter describes the method to characterize plasma membrane sphingomyelin-rich and cholesterol-rich lipid domains by quantitative microscopy. This Chapter also compares different permeabilization methods to visualize intracellular lipid domains.


Subject(s)
Cholesterol , Sphingomyelins , Sphingomyelins/chemistry , Sphingomyelins/metabolism , Cholesterol/chemistry , Cholesterol/metabolism , Humans , Animals , Membrane Microdomains/metabolism , Membrane Microdomains/chemistry , Microscopy/methods , Carrier Proteins/chemistry , Carrier Proteins/metabolism , Cell Membrane/metabolism , Cell Membrane/chemistry
7.
Nat Commun ; 15(1): 5374, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38918400

ABSTRACT

Photothermal microscopy is a highly sensitive pump-probe method for mapping nanostructures and molecules through the detection of local thermal gradients. While visible photothermal microscopy and mid-infrared photothermal microscopy techniques have been developed, they possess inherent limitations. These techniques either lack chemical specificity or encounter significant light attenuation caused by water absorption. Here, we present an overtone photothermal (OPT) microscopy technique that offers high chemical specificity, detection sensitivity, and spatial resolution by employing a visible probe for local heat detection in the C-H overtone region. We demonstrate its capability for high-fidelity chemical imaging of polymer nanostructures, depth-resolved intracellular chemical mapping of cancer cells, and imaging of multicellular C. elegans organisms and highly scattering brain tissues. By bridging the gap between visible and mid-infrared photothermal microscopy, OPT establishes a new modality for high-resolution and high-sensitivity chemical imaging. This advancement complements large-scale shortwave infrared imaging approaches, facilitating multiscale structural and chemical investigations of materials and biological metabolism.


Subject(s)
Caenorhabditis elegans , Microscopy , Animals , Microscopy/methods , Humans , Vibration , Nanostructures/chemistry , Brain/diagnostic imaging , Polymers/chemistry , Cell Line, Tumor
8.
BMC Med Imaging ; 24(1): 158, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38914942

ABSTRACT

BACKGROUND: The assessment of in vitro wound healing images is critical for determining the efficacy of the therapy-of-interest that may influence the wound healing process. Existing methods suffer significant limitations, such as user dependency, time-consuming nature, and lack of sensitivity, thus paving the way for automated analysis approaches. METHODS: Hereby, three structurally different variations of U-net architectures based on convolutional neural networks (CNN) were implemented for the segmentation of in vitro wound healing microscopy images. The developed models were fed using two independent datasets after applying a novel augmentation method aimed at the more sensitive analysis of edges after the preprocessing. Then, predicted masks were utilized for the accurate calculation of wound areas. Eventually, the therapy efficacy-indicator wound areas were thoroughly compared with current well-known tools such as ImageJ and TScratch. RESULTS: The average dice similarity coefficient (DSC) scores were obtained as 0.958 ∼ 0.968 for U-net-based deep learning models. The averaged absolute percentage errors (PE) of predicted wound areas to ground truth were 6.41%, 3.70%, and 3.73%, respectively for U-net, U-net++, and Attention U-net, while ImageJ and TScratch had considerable averaged error rates of 22.59% and 33.88%, respectively. CONCLUSIONS: Comparative analyses revealed that the developed models outperformed the conventional approaches in terms of analysis time and segmentation sensitivity. The developed models also hold great promise for the prediction of the in vitro wound area, regardless of the therapy-of-interest, cell line, magnification of the microscope, or other application-dependent parameters.


Subject(s)
Deep Learning , Image Processing, Computer-Assisted , Microscopy , Wound Healing , Microscopy/methods , Humans , Image Processing, Computer-Assisted/methods , Neural Networks, Computer
9.
ACS Appl Mater Interfaces ; 16(25): 32078-32086, 2024 Jun 26.
Article in English | MEDLINE | ID: mdl-38865735

ABSTRACT

The traditional recognition of extracellular matrix (ECM) at tissue sections relies on the time-consuming immunofluorescence that could not meet the demand of rapid diagnosis. Herein, we introduce a thickness-resolved electrochemiluminescence (ECL) microscopy to image thin-layer ECM at tissue sections for fast histopathological analysis. The unique surface-confined ECL mechanism enables to unveil the diversity and complexity of multiple tissue structures with varying thicknesses. Notably, the short lifetimes and the limited diffusion of electrogenerated coreactant radicals combined with their chemical reactivity result in a 2-fold increase in ECL intensity on ECM structures compared to the remaining tissue, enabling ECM visualization without specific labeling. The further quantitation of the ECM localization within tissue sections furnishes crucial insights into tumor progression and, more importantly, differentiates carcinoma and paracancerous tissues from patients in less than 30 min. Moreover, the reported electrochemistry-based microscopy is a dynamic approach allowing to investigate the transport, tortuosity, and trafficking properties through the tissues. This thickness-resolved recognition strategy not only opens new avenues for imaging complex samples but also holds promise for expediting tissue pathologic diagnosis, offering a more automated protocol with enhanced quantitative data compared to current intraoperative pathology methods.


Subject(s)
Electrochemical Techniques , Extracellular Matrix , Neoplasms , Humans , Extracellular Matrix/chemistry , Extracellular Matrix/metabolism , Electrochemical Techniques/methods , Neoplasms/diagnosis , Neoplasms/pathology , Neoplasms/diagnostic imaging , Neoplasms/metabolism , Luminescent Measurements/methods , Microscopy/methods
10.
J Biomed Opt ; 29(7): 076501, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38912214

ABSTRACT

Significance: Information about the spatial organization of fibers within a nerve is crucial to our understanding of nerve anatomy and its response to neuromodulation therapies. A serial block-face microscopy method [three-dimensional microscopy with ultraviolet surface excitation (3D-MUSE)] has been developed to image nerves over extended depths ex vivo. To routinely visualize and track nerve fibers in these datasets, a dedicated and customizable software tool is required. Aim: Our objective was to develop custom software that includes image processing and visualization methods to perform microscopic tractography along the length of a peripheral nerve sample. Approach: We modified common computer vision algorithms (optic flow and structure tensor) to track groups of peripheral nerve fibers along the length of the nerve. Interactive streamline visualization and manual editing tools are provided. Optionally, deep learning segmentation of fascicles (fiber bundles) can be applied to constrain the tracts from inadvertently crossing into the epineurium. As an example, we performed tractography on vagus and tibial nerve datasets and assessed accuracy by comparing the resulting nerve tracts with segmentations of fascicles as they split and merge with each other in the nerve sample stack. Results: We found that a normalized Dice overlap ( Dice norm ) metric had a mean value above 0.75 across several millimeters along the nerve. We also found that the tractograms were robust to changes in certain image properties (e.g., downsampling in-plane and out-of-plane), which resulted in only a 2% to 9% change to the mean Dice norm values. In a vagus nerve sample, tractography allowed us to readily identify that subsets of fibers from four distinct fascicles merge into a single fascicle as we move ∼ 5 mm along the nerve's length. Conclusions: Overall, we demonstrated the feasibility of performing automated microscopic tractography on 3D-MUSE datasets of peripheral nerves. The software should be applicable to other imaging approaches. The code is available at https://github.com/ckolluru/NerveTracker.


Subject(s)
Nerve Fibers , Software , Imaging, Three-Dimensional/methods , Algorithms , Animals , Image Processing, Computer-Assisted/methods , Tibial Nerve/diagnostic imaging , Vagus Nerve/diagnostic imaging , Microscopy, Ultraviolet/methods , Microscopy/methods
11.
PLoS Negl Trop Dis ; 18(6): e0012279, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38889190

ABSTRACT

BACKGROUND: The standard diagnosis of Ascaris lumbricoides and other soil-transmitted helminth (STH) infections relies on the detection of worm eggs by copromicroscopy. However, this method is dependent on worm patency and shows only limited accuracy in low-intensity infection settings. We aimed to decipher the diagnostic accuracy of different antibodies using various Ascaris antigens in reference to copromicroscopy and quantitative PCR (qPCR), four months after national STH preventative chemotherapy among school children in western Kenya. METHODOLOGY: STH infection status of 390 school children was evaluated via copromicroscopy (Kato-Katz and mini-FLOTAC) and qPCR. In parallel, Ascaris-specific antibody profiles against larval and adult worm lysates, and adult worm excretory-secretory (ES) products were determined by enzyme-linked immunosorbent assay. Antibody cross-reactivity was evaluated using the closely related zoonotic roundworm species Toxocara cati and Toxocara canis. The diagnostic accuracy of each antibody was evaluated using receiver operating curve analysis and the correspondent area under the curve (AUC). PRINCIPAL FINDINGS: Ascaris was the predominant helminth infection with an overall prevalence of 14.9% (58/390). The sensitivity of mini-FLOTAC and Kato-Katz for Ascaris diagnosis reached only 53.5% and 63.8%, respectively compared to qPCR. Although being more sensitive, qPCR values correlated with microscopic egg counts (R = -0.71, P<0.001), in contrast to antibody levels. Strikingly, IgG antibodies recognizing the ES products of adult Ascaris worms reliably diagnosed active Ascaris infection as determined by qPCR and microscopy, with IgG1 displaying the highest accuracy (AUC = 0.83, 95% CI: 0.75-0.91). CONCLUSION: IgG1 antibody responses against adult Ascaris-ES products hold a promising potential for complementing the standard fecal and molecular techniques employed for monitoring Ascaris infections. This is of particular importance in the context of deworming programs as the antibody diagnostic accuracy was independent of egg counts.


Subject(s)
Antibodies, Helminth , Ascariasis , Feces , Sensitivity and Specificity , Ascariasis/diagnosis , Ascariasis/epidemiology , Ascariasis/immunology , Humans , Antibodies, Helminth/blood , Animals , Child , Feces/parasitology , Female , Male , Kenya/epidemiology , Adolescent , Microscopy/methods , Multiplex Polymerase Chain Reaction/methods , Real-Time Polymerase Chain Reaction/methods , Ascaris lumbricoides/immunology , Ascaris lumbricoides/isolation & purification , Antigens, Helminth/immunology , Enzyme-Linked Immunosorbent Assay/methods , Ascaris/immunology , Ascaris/isolation & purification , Endemic Diseases
12.
Trends Parasitol ; 40(7): 633-646, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38824067

ABSTRACT

Microscopy image analysis plays a pivotal role in parasitology research. Deep learning (DL), a subset of artificial intelligence (AI), has garnered significant attention. However, traditional DL-based methods for general purposes are data-driven, often lacking explainability due to their black-box nature and sparse instructional resources. To address these challenges, this article presents a comprehensive review of recent advancements in knowledge-integrated DL models tailored for microscopy image analysis in parasitology. The massive amounts of human expert knowledge from parasitologists can enhance the accuracy and explainability of AI-driven decisions. It is expected that the adoption of knowledge-integrated DL models will open up a wide range of applications in the field of parasitology.


Subject(s)
Artificial Intelligence , Image Processing, Computer-Assisted , Microscopy , Parasitology , Parasitology/methods , Parasitology/instrumentation , Parasitology/trends , Microscopy/instrumentation , Microscopy/methods , Microscopy/standards , Humans , Image Processing, Computer-Assisted/instrumentation , Image Processing, Computer-Assisted/methods , Deep Learning
13.
Malar J ; 23(1): 200, 2024 Jun 28.
Article in English | MEDLINE | ID: mdl-38943203

ABSTRACT

BACKGROUND: Microscopic detection of malaria parasites is labour-intensive, time-consuming, and expertise-demanding. Moreover, the slide interpretation is highly dependent on the staining technique and the technician's expertise. Therefore, there is a growing interest in next-generation, fully- or semi-integrated microscopes that can improve slide preparation and examination. This study aimed to evaluate the clinical performance of miLab™ (Noul Inc., Republic of Korea), a fully-integrated automated microscopy device for the detection of malaria parasites in symptomatic patients at point-of-care in Sudan. METHODS: This was a prospective, case-control diagnostic accuracy study conducted in primary health care facilities in rural Khartoum, Sudan in 2020. According to the outcomes of routine on-site microscopy testing, 100 malaria-positive and 90 malaria-negative patients who presented at the health facility and were 5 years of age or older were enrolled consecutively. All consenting patients underwent miLab™ testing and received a negative or suspected result. For the primary analysis, the suspected results were regarded as positive (automated mode). For the secondary analysis, the operator reviewed the suspected results and categorized them as either negative or positive (corrected mode). Nested polymerase chain reaction (PCR) was used as the reference standard, and expert light microscopy as the comparator. RESULTS: Out of the 190 patients, malaria diagnosis was confirmed by PCR in 112 and excluded in 78. The sensitivity of miLab™ was 91.1% (95% confidence interval [CI] 84.2-95.6%) and the specificity was 66.7% (95% Cl 55.1-67.7%) in the automated mode. The specificity increased to 96.2% (95% Cl 89.6-99.2%), with operator intervention in the corrected mode. Concordance of miLab with expert microscopy was substantial (kappa 0.65 [95% CI 0.54-0.76]) in the automated mode, but almost perfect (kappa 0.97 [95% CI 0.95-0.99]) in the corrected mode. A mean difference of 0.359 was found in the Bland-Altman analysis of the agreement between expert microscopy and miLab™ for quantifying parasite counts. CONCLUSION: When used in a clinical context, miLab™ demonstrated high sensitivity but low specificity. Expert intervention was shown to be required to improve the device's specificity in its current version. miLab™ in the corrected mode performed similar to expert microscopy. Before clinical application, more refinement is needed to ensure full workflow automation and eliminate human intervention. Trial registration ClinicalTrials.gov: NCT04558515.


Subject(s)
Malaria , Microscopy , Point-of-Care Systems , Sensitivity and Specificity , Sudan , Microscopy/methods , Humans , Case-Control Studies , Prospective Studies , Female , Male , Child , Child, Preschool , Adult , Adolescent , Malaria/diagnosis , Young Adult , Middle Aged
14.
Mil Med Res ; 11(1): 38, 2024 Jun 13.
Article in English | MEDLINE | ID: mdl-38867274

ABSTRACT

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.


Subject(s)
Cell Tracking , Holography , Microscopy , Holography/methods , Microscopy/methods , Humans , Cell Tracking/methods , Image Processing, Computer-Assisted/methods , Imaging, Three-Dimensional/methods , Quantitative Phase Imaging
15.
Philos Trans A Math Phys Eng Sci ; 382(2274): 20230257, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38826050

ABSTRACT

The OpenFlexure Microscope is an accessible, three-dimensional-printed robotic microscope, with sufficient image quality to resolve diagnostic features including parasites and cancerous cells. As access to lab-grade microscopes is a major challenge in global healthcare, the OpenFlexure Microscope has been developed to be manufactured, maintained and used in remote environments, supporting point-of-care diagnosis. The steps taken in transforming the hardware and software from an academic prototype towards an accepted medical device include addressing technical and social challenges, and are key for any innovation targeting improved effectiveness in low-resource healthcare. This article is part of the Theo Murphy meeting issue 'Open, reproducible hardware for microscopy'.


Subject(s)
Microscopy , Microscopy/instrumentation , Microscopy/methods , Humans , Robotics/instrumentation , Robotics/trends , Robotics/statistics & numerical data , Equipment Design , Printing, Three-Dimensional/instrumentation , Delivery of Health Care , Software , Point-of-Care Systems
17.
Nat Commun ; 15(1): 5112, 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38879641

ABSTRACT

Virus infectivity is traditionally determined by endpoint titration in cell cultures, and requires complex processing steps and human annotation. Here we developed an artificial intelligence (AI)-powered automated framework for ready detection of virus-induced cytopathic effect (DVICE). DVICE uses the convolutional neural network EfficientNet-B0 and transmitted light microscopy images of infected cell cultures, including coronavirus, influenza virus, rhinovirus, herpes simplex virus, vaccinia virus, and adenovirus. DVICE robustly measures virus-induced cytopathic effects (CPE), as shown by class activation mapping. Leave-one-out cross-validation in different cell types demonstrates high accuracy for different viruses, including SARS-CoV-2 in human saliva. Strikingly, DVICE exhibits virus class specificity, as shown with adenovirus, herpesvirus, rhinovirus, vaccinia virus, and SARS-CoV-2. In sum, DVICE provides unbiased infectivity scores of infectious agents causing CPE, and can be adapted to laboratory diagnostics, drug screening, serum neutralization or clinical samples.


Subject(s)
Artificial Intelligence , Cytopathogenic Effect, Viral , Microscopy , SARS-CoV-2 , Humans , SARS-CoV-2/pathogenicity , SARS-CoV-2/physiology , Microscopy/methods , COVID-19/virology , Neural Networks, Computer , Animals , Vaccinia virus/physiology , Vaccinia virus/pathogenicity , Saliva/virology , Chlorocebus aethiops , Vero Cells , Rhinovirus/pathogenicity , Rhinovirus/physiology , Cell Line
18.
BMC Med Imaging ; 24(1): 152, 2024 Jun 18.
Article in English | MEDLINE | ID: mdl-38890604

ABSTRACT

BACKGROUND: Leishmaniasis is a vector-born neglected parasitic disease belonging to the genus Leishmania. Out of the 30 Leishmania species, 21 species cause human infection that affect the skin and the internal organs. Around, 700,000 to 1,000,000 of the newly infected cases and 26,000 to 65,000 deaths are reported worldwide annually. The disease exhibits three clinical presentations, namely, the cutaneous, muco-cutaneous and visceral Leishmaniasis which affects the skin, mucosal membrane and the internal organs, respectively. The relapsing behavior of the disease limits its diagnosis and treatment efficiency. The common diagnostic approaches follow subjective, error-prone, repetitive processes. Despite, an ever pressing need for an accurate detection of Leishmaniasis, the research conducted so far is scarce. In this regard, the main aim of the current research is to develop an artificial intelligence based detection tool for the Leishmaniasis from the Geimsa-stained microscopic images using deep learning method. METHODS: Stained microscopic images were acquired locally and labeled by experts. The images were augmented using different methods to prevent overfitting and improve the generalizability of the system. Fine-tuned Faster RCNN, SSD, and YOLOV5 models were used for object detection. Mean average precision (MAP), precision, and Recall were calculated to evaluate and compare the performance of the models. RESULTS: The fine-tuned YOLOV5 outperformed the other models such as Faster RCNN and SSD, with the MAP scores, of 73%, 54% and 57%, respectively. CONCLUSION: The currently developed YOLOV5 model can be tested in the clinics to assist the laboratorists in diagnosing Leishmaniasis from the microscopic images. Particularly, in low-resourced healthcare facilities, with fewer qualified medical professionals or hematologists, our AI support system can assist in reducing the diagnosing time, workload, and misdiagnosis. Furthermore, the dataset collected by us will be shared with other researchers who seek to improve upon the detection system of the parasite. The current model detects the parasites even in the presence of the monocyte cells, but sometimes, the accuracy decreases due to the differences in the sizes of the parasite cells alongside the blood cells. The incorporation of cascaded networks in future and the quantification of the parasite load, shall overcome the limitations of the currently developed system.


Subject(s)
Azure Stains , Deep Learning , Microscopy , Humans , Microscopy/methods , Leishmaniasis/diagnostic imaging , Leishmaniasis/parasitology , Leishmania/isolation & purification
19.
BMC Infect Dis ; 24(1): 551, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38824500

ABSTRACT

BACKGROUND: Leishmaniasis, an illness caused by protozoa, accounts for a substantial number of human fatalities globally, thereby emerging as one of the most fatal parasitic diseases. The conventional methods employed for detecting the Leishmania parasite through microscopy are not only time-consuming but also susceptible to errors. Therefore, the main objective of this study is to develop a model based on deep learning, a subfield of artificial intelligence, that could facilitate automated diagnosis of leishmaniasis. METHODS: In this research, we introduce LeishFuNet, a deep learning framework designed for detecting Leishmania parasites in microscopic images. To enhance the performance of our model through same-domain transfer learning, we initially train four distinct models: VGG19, ResNet50, MobileNetV2, and DenseNet 169 on a dataset related to another infectious disease, COVID-19. These trained models are then utilized as new pre-trained models and fine-tuned on a set of 292 self-collected high-resolution microscopic images, consisting of 138 positive cases and 154 negative cases. The final prediction is generated through the fusion of information analyzed by these pre-trained models. Grad-CAM, an explainable artificial intelligence technique, is implemented to demonstrate the model's interpretability. RESULTS: The final results of utilizing our model for detecting amastigotes in microscopic images are as follows: accuracy of 98.95 1.4%, specificity of 98 2.67%, sensitivity of 100%, precision of 97.91 2.77%, F1-score of 98.92 1.43%, and Area Under Receiver Operating Characteristic Curve of 99 1.33. CONCLUSION: The newly devised system is precise, swift, user-friendly, and economical, thus indicating the potential of deep learning as a substitute for the prevailing leishmanial diagnostic techniques.


Subject(s)
Deep Learning , Leishmania , Leishmaniasis , Microscopy , Telemedicine , Humans , Leishmaniasis/parasitology , Leishmaniasis/diagnosis , Leishmania/isolation & purification , Microscopy/methods , COVID-19 , SARS-CoV-2/isolation & purification
20.
BMC Ophthalmol ; 24(1): 241, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38853245

ABSTRACT

BACKGROUND: To compare the effects of a 3D head-up system and microscope eyepiece-assisted simulated vitrectomy intraocular illumination on the ocular surface of an operator. METHODS: This was a prospective randomized controlled study. According to the application system, thirty ophthalmic operators (60 eyes) were randomly divided into 3D and eyepiece groups. Under different intensities of intraocular illumination, operators in both groups viewed the fundus model through a 3D display screen or microscopic eyepiece for 2 h. Objective examinations and a subjective symptom questionnaire were used immediately after the test to evaluate the ocular surface of the operators. Objective examinations included nonintrusion tear meniscus height (NIKTMH), nonintrusion break-up time (NIKBUT), and bulbar redness and strip meniscometry tube (SMTube) measurements. Statistical analyses were performed by using SPSS 26.0 software. RESULTS: After the test, the NIKTMH, NIKBUT and SMTube measurements decreased; however, the degree of change varied among the groups of different systems. The differences between the 3D group and the eyepiece group in NIKTMH measurements, SMTube measurements, subjective symptom scores (eye dryness, difficulty focusing, and cervical pain), and light intensity reaching the ocular surface of the operators were statistically significant (P < 0.05). All of the objective and subjective tests showed that the 3D group had fewer effects on the NIKTMH and SMTube measurements, and the subjective comfort of the 3D group was greater. CONCLUSION: For both 3D screens and eyepieces, simulated vitrectomy with intraocular illumination for two hours can lead to discomfort and abnormalities in the operator's ocular surface; however, these abnormalities are less severe in the 3D group. TRIAL REGISTRATION: This trial was registered on December 22, 2022, at the Chinese Clinical Trials Registry with NO. ChiCTR2200066989.


Subject(s)
Imaging, Three-Dimensional , Vitrectomy , Humans , Vitrectomy/methods , Vitrectomy/instrumentation , Prospective Studies , Male , Female , Adult , Lighting/instrumentation , Tears , Microscopy/methods , Dry Eye Syndromes
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