open-source-miniature-fluorimeter-to-monitor-real-time-isothermal

Open-Source Miniature Fluorimeter to Monitor Real-Time Isothermal Nucleic Acid Amplification Reactions in Resource-Limited Settings

Traditional methods to detect and quantify nucleic acids rely on polymerase chain reaction (PCR) and require the use of expensive thermocyclers with ...

Rice University

A modular video endoscope is developed to enable both white light imaging (WLI) and vital-dye fluorescence imaging (VFI) in a single-endoscopic insertion for the early detection of cancer in Barrett’s esophagus (BE). We demonstrate that VFI can be achieved in conjunction with white light endoscopy, where appropriate white balance is used to correct for the presence of the emission filter. In VFI mode, a contrast enhancement feature is implemented in real time to further highlight glandular patterns in BE and related malignancies without introducing artifacts. In a pilot study, we demonstrate accurate correlation of images in two widefield modalities, with representative images showing the disruption and effacement of glandular architecture associated with cancer development in BE. VFI images of these alterations exhibit enhanced contrast when compared to WLI. Results suggest that the usefulness of VFI in the detection of BE-related neoplasia should be further evaluated in future in vivo studies.

In vivo white light and contrast-enhanced vital-dye fluorescence imaging of Barrett's-related neoplasia in a single-endoscopic insertion.

Fiber-optic endomicroscopy is a minimally invasive method to image cellular morphology in vivo. Using a coherent fiber bundle as an image relay, it allows additional imaging optics to be placed at the distal end of the fiber outside the body. In this research, we use this approach to demonstrate a compact, low-cost line-scanning confocal fluorescence microendoscope that can be constructed for <$5000. Confocal imaging is enabled without the need for mechanical scanning by synchronizing a digital light projector with the rolling shutter of a CMOS camera. Its axial performance is characterized in comparison with a nonscanned high-resolution microendoscope. We validate the optical sectioning capability of the microendoscope by imaging a two-dimensional phantom and ex vivo mouse esophageal and colon tissues. Results show that optical sectioning using this approach improves visualization of nuclear morphometry and suggest that this low-cost line-scanning microendoscope can be used to evaluate various pathological conditions.

Line-scanning confocal microendoscope for nuclear morphometry imaging.

Colonoscopy is routinely performed for colorectal cancer screening but lacks the capability to accurately characterize precursor lesions and early cancers. High-resolution microendoscopy (HRME) is a low-cost imaging tool to visualize colorectal polyps with subcellular resolution. We present a computer-aided algorithm to evaluate HRME images of colorectal polyps and classify neoplastic from benign lesions. Using histopathology as the gold standard, clinically relevant features based on luminal morphology and texture are quantified to build the classification algorithm. We demonstrate that adenomatous polyps can be identified with a sensitivity and specificity of 100% and 80% using a two-feature linear discriminant model in a pilot test set. The classification algorithm presented here offers an objective framework to detect adenomatous lesions in the colon with high accuracy and can potentially improve real-time assessment of colorectal polyps.

Quantitative analysis of in vivo high-resolution microendoscopic images for the detection of neoplastic colorectal polyps.

Fiber-optic endomicroscopy is a minimally invasive tool to probe disease progression with subcellular resolution. In this Letter, we demonstrate a low-cost and compact fluorescence microendoscope capable of line-scanning confocal imaging by synchronizing a digital light projector with a CMOS camera. We present the digital aperture design to enable real-time confocal imaging, and we implement parallel illumination to improve the optical sectioning performance. Furthermore, we show that the confocal microendoscope can enhance visualization of disease-associated features when imaging highly scattering esophageal specimens.

Improving nuclear morphometry imaging with real-time and low-cost line-scanning confocal microendoscope.

Line-scanning confocal microendoscopy offers video-rate cellular imaging of scattering tissue with relatively simple hardware, but its axial response is inferior to that of point-scanning systems. Based on Fourier optics theory, we designed differential confocal apertures with a simple subtraction technique to improve the line-scanning sectioning performance. Taking advantage of digital slit apertures on a digital light projector and a CMOS rolling shutter, we demonstrate real-time optical sectioning performance comparable to point scanning in a dual-camera microendoscope (<$6,000). We validate the background rejection capability when imaging porcine columnar epithelium stained with fluorescent contrast agents with different uptake mechanisms and staining properties.

Simple differential digital confocal aperture to improve axial response of line-scanning confocal microendoscopes.

Cervical cancer incidence and mortality rates remain high in medically underserved areas. In this study, we present a low-cost (<$5,000), portable and user-friendly confocal microendoscope, and we report on its clinical use to image precancerous lesions in the cervix. The confocal microendoscope employs digital apertures on a digital light projector and a CMOS sensor to implement line-scanning confocal imaging. Leveraging its versatile programmability, we describe an automated aperture alignment algorithm to ensure clinical ease-of-use and to facilitate technology dissemination in low-resource settings. Imaging performance is then evaluated in  and  pilot studies; results demonstrate that the confocal microendoscope can enhance visualization of nuclear morphology, contributing to significantly improved recognition of clinically important features for detection of cervical precancer.

In vivo imaging of cervical precancer using a low-cost and easy-to-use confocal microendoscope.

Optical endoscopy is the primary diagnostic and therapeutic tool for management of gastrointestinal (GI) malignancies. Most GI neoplasms arise from precancerous lesions; thus, technical innovations to improve detection and diagnosis of precancerous lesions and early cancers play a pivotal role in improving outcomes. Over the last few decades, the field of GI endoscopy has witnessed enormous and focused efforts to develop and translate accurate, user-friendly, and minimally invasive optical imaging modalities. From a technical point of view, a wide range of novel optical techniques is now available to probe different aspects of light-tissue interaction at macroscopic and microscopic scales, complementing white light endoscopy. Most of these new modalities have been successfully validated and translated to routine clinical practice. Herein, we provide a technical review of the current status of existing and promising new optical endoscopic imaging technologies for GI cancer screening and surveillance. We summarize the underlying principles of light-tissue interaction, the imaging performance at different scales, and highlight what is known about clinical applicability and effectiveness. Furthermore, we discuss recent discovery and translation of novel molecular probes that have shown promise to augment endoscopists' ability to diagnose GI lesions with high specificity. We also review and discuss the role and potential clinical integration of artificial intelligence-based algorithms to provide decision support in real time. Finally, we provide perspectives on future technology development and its potential to transform endoscopic GI cancer detection and diagnosis.

Advances in optical gastrointestinal endoscopy: a technical review.

 Conventional cystoscopy plays an important role in detection of bladder cancer; however, it is difficult to differentiate benign and neoplastic lesions based on cystoscopic appearance alone. Advanced microscopic modalities, such as confocal laser endomicroscopy and optical coherence tomography, have been shown to provide critical histopathologic information to help identify neoplastic bladder lesions in real time, but their availability and clinical adoption are limited due to a high cost. In this study, we present the first use of a novel and low-cost ($ <5000) confocal high-resolution microendoscope (confocal HRME) for  imaging of bladder lesions.  In a cohort of 15 patients undergoing white light cystoscopy as part of their standard of care, high-resolution images of proflavine-stained bladder lesions were acquired  using the confocal HRME. Based on these images, we evaluated the ability of the confocal HRME to visualize uroepithelium with subcellular resolution and high contrast. Furthermore, we analyzed the cellular architecture and staining patterns of benign and neoplastic bladder lesions in confocal HRME images and compared results to that of standard cystoscopy and histopathology.  imaging in the pilot study demonstrates that the confocal HRME resolved subcellular structures of bladder uroepithelium with high contrast. In a wide range of clinical conditions from normal bladder wall to benign and neoplastic lesions, confocal HRME images revealed important diagnostic features that correlated to histopathology.  The confocal HRME provides an affordable, portable, and easy-to-use tool to allow real-time and high-contrast subcellular characterization of bladder lesions, well suited for bladder cancer detection in community and resource-constrained settings. The ClinicalTrials.gov Identifier: NCT02340650.

Initial Results of First  Imaging of Bladder Lesions Using a High-Resolution Confocal Microendoscope.

Microscopic evaluation of resected tissue plays a central role in the surgical management of cancer. Because optical microscopes have a limited depth-of-field (DOF), resected tissue is either frozen or preserved with chemical fixatives, sliced into thin sections placed on microscope slides, stained, and imaged to determine whether surgical margins are free of tumor cells-a costly and time- and labor-intensive procedure. Here, we introduce a deep-learning extended DOF (DeepDOF) microscope to quickly image large areas of freshly resected tissue to provide histologic-quality images of surgical margins without physical sectioning. The DeepDOF microscope consists of a conventional fluorescence microscope with the simple addition of an inexpensive (less than $10) phase mask inserted in the pupil plane to encode the light field and enhance the depth-invariance of the point-spread function. When used with a jointly optimized image-reconstruction algorithm, diffraction-limited optical performance to resolve subcellular features can be maintained while significantly extending the DOF (200 µm). Data from resected oral surgical specimens show that the DeepDOF microscope can consistently visualize nuclear morphology and other important diagnostic features across highly irregular resected tissue surfaces without serial refocusing. With the capability to quickly scan intact samples with subcellular detail, the DeepDOF microscope can improve tissue sampling during intraoperative tumor-margin assessment, while offering an affordable tool to provide histological information from resected tissue specimens in resource-limited settings.

Yubo Tang

Department of Bioengineering

Rice University

Open-Source Miniature Fluorimeter to Monitor Real-Time Isothermal Nucleic Acid Amplification Reactions in Resource-Limited Settings

Yubo Tang

.css-o250i3{font-size:18px;font-family:Open Sans,sans-serif;line-height:21.6px;}Department of Bioengineering

Rice University

Open-Source Miniature Fluorimeter to Monitor Real-Time Isothermal Nucleic Acid Amplification Reactions in Resource-Limited Settings

Department of Bioengineering