Diagnostic evaluation of nested PCR and microscopy for Cryptosporidiosis in goats: can COWP gene based qRT-PCR be useful in assessment of active Cryptosporidial infections?

The present research delved into the transmission patterns, diagnostic methods, molecular traits, and phylogenetic analysis of Cryptosporidium species. The research was undertaken to enhance comprehension of the epidemiology and the potential for zoonotic transmission. A total of 80 goat-kid samples were tested, 7 were confirmed positive by mZN microscopy and 12 by nested-PCR. By PCR, 18SSUrRNA, HSP70, and GP60 amplicons were tested for Cryptosporidium. The restriction enzymes viz., SspI, VspI and MboII were used to genotype 12 Cryptosporidium positive samples by which C. parvum and C. bovis mixed infections were detected. Quantitative reverse transcription real-time PCR was used to transcriptionally screen the COWP-subunit genes to assess the severity of the infection in goat-kids, which showed upregulation of COWP6 and COWP4, while COWP9 and COWP3 genes were downregulated. A silent mutation was found at the codon CCA→CCC, which is being reported for the first time in goat field isolates. Phylogenetic and sequencing analyses confirmed the presence of the anthropozoonotic IIe subtype.

Hyperspectral dark-field microscopy of human breast lumpectomy samples for tumor margin detection in breast-conserving surgery.

Significance: Hyperspectral dark-field microscopy (HSDFM) and data cube analysis algorithms demonstrate successful detection and classification of various tissue types, including carcinoma regions in human post-lumpectomy breast tissues excised during breast-conserving surgeries. Aim: We expand the application of HSDFM to the classification of tissue types and tumor subtypes in pre-histopathology human breast lumpectomy samples. Approach: Breast tissues excised during breast-conserving surgeries were imaged by the HSDFM and analyzed. The performance of the HSDFM is evaluated by comparing the backscattering intensity spectra of polystyrene microbead solutions with the Monte Carlo simulation of the experimental data. For classification algorithms, two analysis approaches, a supervised technique based on the spectral angle mapper (SAM) algorithm and an unsupervised technique based on the K-means algorithm are applied to classify various tissue types including carcinoma subtypes. In the supervised technique, the SAM algorithm with manually extracted endmembers guided by H&E annotations is used as reference spectra, allowing for segmentation maps with classified tissue types including carcinoma subtypes. Results: The manually extracted endmembers of known tissue types and their corresponding threshold spectral correlation angles for classification make a good reference library that validates endmembers computed by the unsupervised K-means algorithm. The unsupervised K-means algorithm, with no a priori information, produces abundance maps with dominant endmembers of various tissue types, including carcinoma subtypes of invasive ductal carcinoma and invasive mucinous carcinoma. The two carcinomas' unique endmembers produced by the two methods agree with each other within <2% residual error margin. Conclusions: Our report demonstrates a robust procedure for the validation of an unsupervised algorithm with the essential set of parameters based on the ground truth, histopathological information. We have demonstrated that a trained library of the histopathology-guided endmembers and associated threshold spectral correlation angles computed against well-defined reference data cubes serve such parameters. Two classification algorithms, supervised and unsupervised algorithms, are employed to identify regions with carcinoma subtypes of invasive ductal carcinoma and invasive mucinous carcinoma present in the tissues. The two carcinomas' unique endmembers used by the two methods agree to <2% residual error margin. This library of high quality and collected under an environment with no ambient background may be instrumental to develop or validate more advanced unsupervised data cube analysis algorithms, such as effective neural networks for efficient subtype classification.

Two cases with discrepancy in the quantitative cytological assessment of cerebrospinal fluid in neonatal samples using light microscopy in comparison with Sysmex XN-1000.

We present two cases from the neonatal department with cerebrospinal fluid examination. We revealed a striking discrepancy in polymorphonuclear (PMN) and mononuclear (MN) cell counts using conventional light microscopy in comparison with automated analyzer Sysmex XN-1000 (PMNs - 13 vs. 173x106/L, MNs - 200 vs. 67x106/L in case 1 and PMNs - 13 vs. 372x106/L, MNs - 411 vs. 179x106/L in case 2). We revealed the dominant presence of hemosiderophages in both cases in cytospin slide. Even though Sysmex XN-1000 offers fast examination with a low sample volume, there is possibility of misdiagnosis, with negative impact on the patient.

Efficient Assessment of Tumor Vascular Shutdown by Photodynamic Therapy on Orthotopic Pancreatic Cancer Using High-Speed Wide-Field Waterproof Galvanometer Scanner Photoacoustic Microscopy.

To identify the vascular alteration by photodynamic therapy (PDT), the utilization of high-resolution, high-speed, and wide-field photoacoustic microscopy (PAM) has gained enormous interest. The rapid changes in vasculature during PDT treatment and monitoring of tumor tissue activation in the orthotopic pancreatic cancer model have received limited attention in previous studies. Here, a fully two-axes waterproof galvanometer scanner-based photoacoustic microscopy (WGS-PAM) system was developed for in vivo monitoring of dynamic variations in micro blood vessels due to PDT in an orthotopic pancreatic cancer mouse model. The photosensitizer (PS), Chlorin e6 (Ce6), was utilized to activate antitumor reactions in response to the irradiation of a 660 nm light source. Microvasculatures of angiogenesis tissue were visualized on a 40 mm2 area using the WGS-PAM system at 30 min intervals for 3 h after the PDT treatment. The decline in vascular intensity was observed at 24.5% along with a 32.4% reduction of the vascular density at 3 h post-PDT by the analysis of PAM images. The anti-vascularization effect was also identified with fluorescent imaging. Moreover, Ce6-PDT increased apoptotic and necrotic markers while decreasing vascular endothelial growth factor (VEGF) expression in MIA PaCa-2 and BxPC-3 pancreatic cancer cell lines. The approach of the WGS-PAM system shows the potential to investigate PDT effects on the mechanism of angiographic dynamics with high-resolution wide-field imaging modalities.

Oxygen Assessment in Tumors In Vivo Using Phosphorescence Lifetime Imaging Microscopy.

The oxygen level in a tumor is a crucial factor for its development and response to therapies. Phosphorescence lifetime imaging (PLIM) with the use of phosphorescent oxygen probes is a highly sensitive, noninvasive optical technique for the assessment of molecular oxygen in living cells and tissues. Here, we present a protocol for microscopic mapping of oxygen distribution in a mouse tumor model in vivo. We demonstrate that PLIM microscopy, in combination with an Ir(III)-based probe, enables visualization of cellular-level heterogeneity of tumor oxygenation.

Label-free assessment of pathological changes in pancreatic intraepithelial neoplasia by biomedical multiphoton microscopy.

Pancreatic intraepithelial neoplasia (PanIN) is the most common precursor lesion that has the potential to progress to invasive pancreatic cancer, and early and rapid detection may offer patients a chance for treatment before the development of invasive carcinoma. Therefore, the identification of PanIN holds significant clinical importance. In this study, we first used multiphoton microscopy (MPM) combining two-photon excitation fluorescence and second-harmonic generation imaging to label-free detect PanIN and attempted to differentiate between normal pancreatic ducts and different grades of PanIN. Then, we also developed an automatic image processing strategy to extract eight morphological features of collagen fibers from MPM images to quantify the changes in collagen fibers surrounding the ducts. Experimental results demonstrate that the combination of MPM and quantitative information can accurately identify normal pancreatic ducts and different grades of PanIN. This study may contribute to the rapid diagnosis of pancreatic diseases and may lay the foundation for further clinical application of MPM.

Compact portable higher harmonic generation microscopy for the real time assessment of unprocessed thyroid tissue.

During thyroid surgery fast and reliable intra-operative pathological feedback has the potential to avoid a two-stage procedure and significantly reduce health care costs in patients undergoing a diagnostic hemithyroidectomy (HT). We explored higher harmonic generation (HHG) microscopy, which combines second harmonic generation (SHG), third harmonic generation (THG), and multiphoton excited autofluorescence (MPEF) for this purpose. With a compact, portable HHG microscope, images of freshly excised healthy tissue, benign nodules (follicular adenoma) and malignant tissue (papillary carcinoma, follicular carcinoma and spindle cell carcinoma) were recorded. The images were generated on unprocessed tissue within minutes and show relevant morphological thyroid structures in good accordance with the histology images. The thyroid follicle architecture, cells, cell nuclei (THG), collagen organization (SHG) and the distribution of thyroglobulin and/or thyroid hormones T3 or T4 (MPEF) could be visualized. We conclude that SHG/THG/MPEF imaging is a promising tool for clinical intraoperative assessment of thyroid tissue.

Physically informed Monte Carlo simulation of dual-wedge prism-based spectroscopic single-molecule localization microscopy.

Significance: The dual-wedge prism (DWP)-based spectroscopic single-molecule localization microscopy (sSMLM) system offers improved localization precision and adjustable spectral or localization performance, but its nonlinear spectral dispersion presents a challenge. A systematic method can help understand the challenges and thereafter optimize the DWP system's performance by customizing the system parameters to maximize the spectral or localization performance for various molecular labels. Aim: We developed a Monte Carlo (MC)-based model that predicts the imaging output of the DWP-based sSMLM system given different system parameters. Approach: We assessed our MC model's localization and spectral precisions by comparing our simulation against theoretical equations and fluorescent microspheres. Furthermore, we simulated the DWP-based system using beamsplitters (BSs) with a reflectance (R):transmittance (T) of R50:T50 and R30:T70 and their tradeoffs. Results: Our MC simulation showed average deviations of 2.5 and 2.1 nm for localization and spectral precisions against theoretical equations and 2.3 and 1.0 nm against fluorescent microspheres. An R30:T70 BS improved the spectral precision by 8% but worsened the localization precision by 35% on average compared with an R50:T50 BS. Conclusions: The MC model accurately predicted the localization precision, spectral precision, spectral peaks, and spectral widths of fluorescent microspheres, as validated by experimental data. Our work enhances the theoretical understanding of DWP-based sSMLM for multiplexed imaging, enabling performance optimization.

Viral enumeration using cost-effective wet-mount epifluorescence microscopy for aquatic ecosystems and modern microbialites.

IMPORTANCE: Low-cost and robust viral enumeration is a critical first step toward understanding the global virome. Our method is a deep drive integration providing a window into viral dark matter within aquatic ecosystems. We enumerated the viruses within Green Lake and Great Salt Lake microbialites, EPS, and water column. The entire weight of all the viruses in Green Lake and Great Salt Lake are ~598 g and ~2.2 kg, respectively.

Cell phone microscopy enabled low-cost manufacturable colorimetric urine glucose test.

Glucose serves as a pivotal biomarker crucial for the monitoring and diagnosis of a spectrum of medical conditions, encompassing hypoglycemia, hyperglycemia, and diabetes, all of which may precipitate severe clinical manifestations in individuals. As a result, there is a growing demand within the medical domain for the development of rapid, cost-effective, and user-friendly diagnostic tools. In this research article, we introduce an innovative glucose sensor that relies on microfluidic devices meticulously crafted from disposable, medical-grade tapes. These devices incorporate glucose urine analysis strips securely affixed to microscope glass slides. The microfluidic channels are intricately created through laser cutting, representing a departure from traditional cleanroom techniques. This approach streamlines production processes, enhances cost-efficiency, and obviates the need for specialized equipment. Subsequent to the absorption of the target solution, the disposable device is enclosed within a 3D-printed housing. Image capture is seamlessly facilitated through the use of a smartphone camera for subsequent colorimetric analysis. Our study adeptly demonstrates the glucose sensor's capability to accurately quantify glucose concentrations within sucrose solutions. This is achieved by employing an exponential regression model, elucidating the intricate relationship between glucose concentrations and average RGB (Red-Green-Blue) values. Furthermore, our comprehensive analysis reveals minimal variation in sensor performance across different instances. Significantly, this study underscores the potential adaptability and versatility of our solution for a wide array of assay types and smartphone-based sensor systems, making it particularly promising for deployment in resource-constrained settings and undeveloped countries. The robust correlation established between glucose concentrations and average RGB values, substantiated by an impressive R-square value of 0.98709, underscores the effectiveness and reliability of our pioneering approach within the medical field.

Unbiased image segmentation assessment toolkit for quantitative differentiation of state-of-the-art algorithms and pipelines.

BACKGROUND: Image segmentation pipelines are commonly used in microscopy to identify cellular compartments like nucleus and cytoplasm, but there are few standards for comparing segmentation accuracy across pipelines. The process of selecting a segmentation assessment pipeline can seem daunting to researchers due to the number and variety of metrics available for evaluating segmentation quality. RESULTS: Here we present automated pipelines to obtain a comprehensive set of 69 metrics to evaluate segmented data and propose a selection methodology for models based on quantitative analysis, dimension reduction or unsupervised classification techniques and informed selection criteria. CONCLUSION: We show that the metrics used here can often be reduced to a small number of metrics that give a more complete understanding of segmentation accuracy, with different groups of metrics providing sensitivity to different types of segmentation error. These tools are delivered as easy to use python libraries, command line tools, Common Workflow Language Tools, and as Web Image Processing Pipeline interactive plugins to ensure a wide range of users can access and use them. We also present how our evaluation methods can be used to observe the changes in segmentations across modern machine learning/deep learning workflows and use cases.

Assessment of coronary microcirculation alterations in a porcine model of no-reflow using ultrasound localization microscopy: a proof of concept study.

BACKGROUND: Coronary microvascular obstruction also known as no-reflow phenomenon is a major issue during myocardial infarction that bears important prognostic implications. Alterations of the microvascular network remains however challenging to assess as there is no imaging modality in the clinics that can image directly the coronary microvascular vessels. Ultrasound Localization Microscopy (ULM) imaging was recently introduced to map microvascular flows at high spatial resolution (∼10 µm). In this study, we developed an approach to image alterations of the microvascular coronary flow in ex vivo perfused swine hearts. METHODS: A porcine model of myocardial ischemia-reperfusion was used to obtain microvascular coronary alterations and no-reflow. Four female hearts with myocardial infarction in addition to 6 controls were explanted and placed immediately in a dedicated preservation and perfusion box manufactured for ultrasound imaging. Microbubbles (MB) were injected into the vasculature to perform Ultrasound Localization Microscopy (ULM) imaging and a linear ultrasound probe mounted on a motorized device was used to scan the heart on multiple slices. The coronary microvascular anatomy and flow velocity was reconstructed using dedicated ULM algorithms and analyzed quantitatively. FINDINGS: We were able to image the coronary microcirculation of ex vivo swine hearts at a resolution of tens of microns and measure flow velocities ranging from 10 mm/s in arterioles up to more than 200 mm/s in epicardial arteries. Under different aortic perfusion pressures, we measured in large arteries of a subset of control hearts an increase of flow velocity from 31 ± 11 mm/s at 87 mmHg to 47 ± 17 mm/s at 132 mmHg (N = 3 hearts, P < 0.05). This increase was compared with a control measurement with a flowmeter in the aorta. We also compared 6 control hearts to 4 hearts in which no-reflow was induced by the occlusion and reperfusion of a coronary artery. Using average MB velocity and average density of MB per unit of surface as two ULM quantitative markers of perfusion, we were able to detect areas of coronary no-reflow in good agreement with a control anatomical pathology analysis of the cardiac tissue. In the no-reflow zone, we measured an average perfusion of 204 ± 305 MB/mm2 compared to 3182 ± 1302 MB/mm2 in the surrounding re-perfused area. INTERPRETATION: We demonstrated this approach can directly image and quantify coronary microvascular obstruction and no-reflow on large mammal perfused hearts. This is a first step for noninvasive, quantitative and affordable assessment of the coronary microcirculation function and particularly coronary microvascular anatomy in the infarcted heart. This approach has the potential to be extended to other clinical situations characterized by microvascular dysfunction. FUNDING: This study was supported by the French National Research Agency (ANR) under ANR-21-CE19-0002 grant agreement.

Investigating Uncertainties in Single-Molecule Localization Microscopy Using Experimentally Informed Monte Carlo Simulation.

Single-molecule localization microscopy (SMLM) enables the visualization of cellular nanostructures in vitro with sub-20 nm resolution. While substructures can generally be imaged with SMLM, the structural understanding of the images remains elusive. To better understand the link between SMLM images and the underlying structure, we developed a Monte Carlo (MC) simulation based on experimental imaging parameters and geometric information to generate synthetic SMLM images. We chose the nuclear pore complex (NPC), a nanosized channel on the nuclear membrane which gates nucleo-cytoplasmic transport of biomolecules, as a test geometry for testing our MC model. Using the MC model to simulate SMLM images, we first optimized our clustering algorithm to separate >106 molecular localizations of fluorescently labeled NPC proteins into hundreds of individual NPCs in each cell. We then illustrated using our MC model to generate cellular substructures with different angles of labeling to inform our structural understanding through the SMLM images obtained.

Blind Image Quality Assessment for Pathological Microscopic Image Under Screen and Immersion Scenarios.

The high-quality pathological microscopic images are essential for physicians or pathologists to make a correct diagnosis. Image quality assessment (IQA) can quantify the visual distortion degree of images and guide the imaging system to improve image quality, thus raising the quality of pathological microscopic images. Current IQA methods are not ideal for pathological microscopy images due to their specificity. In this paper, we present deep learning-based blind image quality assessment model with saliency block and patch block for pathological microscopic images. The saliency block and patch block can handle the local and global distortions, respectively. To better capture the area of interest of pathologists when viewing pathological images, the saliency block is fine-tuned by eye movement data of pathologists. The patch block can capture lots of global information strongly related to image quality via the interaction between different image patches from different positions. The performance of the developed model is validated by the home-made Pathological Microscopic Image Quality Database under Screen and Immersion Scenarios (PMIQD-SIS) and cross-validated by the five public datasets. The results of ablation experiments demonstrate the contribution of the added blocks. The dataset and the corresponding code are publicly available at: https://github.com/mikugyf/PMIQD-SIS.

3D fractures analysis and conservation assessment of wrought iron javelin through advanced non-invasive techniques.

3D imaging is a powerful tool of high resolution and non-destructive imaging technology for the study of ancient weapons and military technology, which reveals the original microstructures and corrosion patterns that threaten these artefacts. Here we report quantitative analysis of the 3D distribution and the orientation of fractures, and uncorroded metal particles within a wrought iron javelin unearthed at the Phoenician-Punic site of Motya, Italy. The study aimed to gain a better understanding of the relationship between corrosion and local stresses within the artifact and to evaluate its manufacturing technology, as well as the effects of post-treatment with Paraloid B72 on concretion and mineralized layers. The cracks were quantified in terms of content, size, and orientation. The condition of artefact storage was evaluated by a multi-analytical approach, including X-ray microscopy, field emission electron microscopy and micro-Raman spectroscopy. The results indicated that a specific technique was used to create a sturdy, lightweight javelin with a central shaft for piercing or thrusting. The fractures appear elongated in the direction of the longitudinal axis of the blade, showing the forging direction of the original metallic block. The study concluded that the artifact had not yet been stabilized due to the presence of lepidocrocite.

Live Stimulated Raman Histology for the Near-Instant Assessment of Central Nervous System Samples.

Central nervous system tumors encompass many heterogeneous neoplasms with different outcomes and treatment strategies. The current classification of these tumors is based on molecular parameters in addition to histopathology to define tumor entities. This genomic characterization of tumors is also becoming increasingly essential for physicians to identify targeted therapy options. The deployment of such genomic profiling relies on an efficient surgical sampling. To perform an appropriate tumor resection and a correct sampling of the tumor, the neurosurgeon may request an intraoperative pathological consultation. Stimulated Raman histology (SRH), an emerging nondestructive imaging technology, can address this challenge. SRH allows for a rapid and label-free microscopic examination of unprocessed tissues samples in near-perfect concordance with standard histology. In this study we showed that SRH enabled the near-instant microscopic examination of various central nervous system samples without any tissue processing such as labeling, freezing nor sectioning. Since SRH imaging is a nondestructive approach, we demonstrated that the tissue could be readily recovered after SRH imaging and reintroduced into the conventional pathology workflow including immunohistochemistry and genomic profiling to establish a definitive diagnosis.

A Low-Cost Modular Imaging System for Rapid, Multiplexed Immunofluorescence Detection in Clinical Tissues.

To image 4-plex immunofluorescence-stained tissue samples at a low cost with cellular level resolution and sensitivity and dynamic range required to detect lowly and highly abundant targets, here we describe a robust, inexpensive (<$9000), 3D printable portable imaging device (Tissue Imager). The Tissue Imager can immediately be deployed on benchtops for in situ protein detection in tissue samples. Applications for this device are broad, ranging from answering basic biological questions to clinical pathology, where immunofluorescence can detect a larger number of markers than the standard H&E or chromogenic immunohistochemistry (CIH) staining, while the low cost also allows usage in classrooms. After characterizing our platform's specificity and sensitivity, we demonstrate imaging of a 4-plex immunology panel in human cutaneous T-cell lymphoma (CTCL) formalin-fixed paraffin-embedded (FFPE) tissue samples. From those images, positive cells were detected using CellProfiler, a popular open-source software package, for tumor marker profiling. We achieved a performance on par with commercial epifluorescence microscopes that are >10 times more expensive than our Tissue Imager. This device enables rapid immunofluorescence detection in tissue sections at a low cost for scientists and clinicians and can provide students with a hands-on experience to understand engineering and instrumentation. We note that for using the Tissue Imager as a medical device in clinical settings, a comprehensive review and approval processes would be required.

Assessment of corneal endothelial cell parameters using specular microscopy in previously infected SARS-CoV-2 patients.

PURPOSE: To examine the long-term effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on the corneal endothelium. METHODS: This was a comparative, cross-sectional study that included subjects who had recovered from SARS-CoV-2 infection for at least 6 months (group 1) and a group of age- and sex-matched controls with no prior symptomatology or documentation of SARS-CoV-2 infection (group 2). After full ophthalmological evaluation, specular microscopy was used to examine the endothelial cell parameters, including endothelial cell density, coefficient of variation, hexagonality, average area, and central corneal thickness. RESULTS: Sixty-four and 53 right eyes were included in groups 1 and 2, respectively. No statistically significant differences were detected in any of the examined specular parameters between the two groups. CONCLUSION: SARS-CoV-2 infection may have no delayed sequel on the corneal endothelium. Future prospective studies with repeated examinations in the same subjects would be useful.