An automated system for whole microscopic image acquisition and analysis

A Microscope Setup and Methodology for Capturing Hyperspectral and RGB Histopathological Imaging Databases

The digitization of pathology departments in hospitals around the world is now a reality. The current commercial solutions applied to digitize histopathological samples consist of a robotic microscope with an RGB-type camera attached to it. This technology is very limited in terms of information captured, as it only works with three spectral bands of the visible electromagnetic spectrum. Therefore, we present an automated system that combines RGB and hyperspectral technology. Throughout this work, the hardware of the system and its components are described along with the developed software and a working methodology to ensure the correct capture of histopathological samples. The software is integrated by the controller of the microscope, which features an autofocus functionality, whole slide scanning with a stitching algorithm, and hyperspectral scanning functionality. As a reference, the time to capture and process a complete sample with 20 regions of high biological interest using the proposed method is estimated at a maximum of 79 min, reducing the time required by a manual operator by at least three times. Both hardware and software can be easily adapted to other systems that might benefit from the advantages of hyperspectral technology.

Dual imaging technique for a real-time inspection system of foreign object detection in fresh-cut vegetables

Fresh-cut vegetables are a food product susceptible to contamination by foreign materials (FMs). To detect a range of potential FMs in fresh-cut vegetables, a dual imaging technique (fluorescence and color imaging) with a simple and effective image processing algorithm in a user-friendly software interface was developed for a real-time inspection system. The inspection system consisted of feeding and sensing units, including two cameras positioned in parallel, illuminations (white LED and UV light), and a conveyor unit. A camera equipped with a long-pass filter was used to collect fluorescence images. Another camera collected color images of fresh-cut vegetables and FMs. The feeding unit fed FMs mixed with fresh-cut vegetables onto a conveyor belt. Two cameras synchronized programmatically in the software interface simultaneously collected fluorescence and color image samples based on the region of interest as they moved through the conveyor belt. Using simple image processing algorithms, FMs could be detected and depicted in two different image windows. The results demonstrated that the dual imaging technique can effectively detect potential FMs in two types of fresh-cut vegetables (cabbage and green onion), as indicated by the combined fluorescence and color imaging accuracy. The test results showed that the real-time inspection system could detect FMs measuring 0.5 mm in fresh-cut vegetables. The results showed that the combined detection accuracy of FMs in the cabbage (95.77%) sample was superior to that of green onion samples (87.89%). Therefore, the inspection system was more effective at detecting FMs in cabbage samples than in green onion samples.

Whole Slide Imaging Technology and Its Applications: Current and Emerging Perspectives

Background. Whole slide imaging (WSI) represents a paradigm shift in pathology, serving as a necessary first step for a wide array of digital tools to enter the field. It utilizes virtual microscopy wherein glass slides are converted into digital slides and are viewed by pathologists by automated image analysis. Its impact on pathology workflow, reproducibility, dissemination of educational material, expansion of service to underprivileged areas, and institutional collaboration exemplifies a significant innovative movement. The recent US Food and Drug Administration approval to WSI for its use in primary surgical pathology diagnosis has opened opportunities for wider application of this technology in routine practice. Main Text. The ongoing technological advances in digital scanners, image visualization methods, and the integration of artificial intelligence-derived algorithms with these systems provide avenues to exploit its applications. Its benefits are innumerable such as ease of access through the internet, avoidance of physical storage space, and no risk of deterioration of staining quality or breakage of slides to name a few. Although the benefits of WSI to pathology practices are many, the complexities of implementation remain an obstacle to widespread adoption. Some barriers including the high cost, technical glitches, and most importantly professional hesitation to adopt a new technology have hindered its use in routine pathology. Conclusions. In this review, we summarize the technical aspects of WSI, its applications in diagnostic pathology, training, and research along with future perspectives. It also highlights improved understanding of the current challenges to implementation, as well as the benefits and successes of the technology. WSI provides a golden opportunity for pathologists to guide its evolution, standardization, and implementation to better acquaint them with the key aspects of this technology and its judicial use. Also, implementation of routine digital pathology is an extra step requiring resources which (currently) does not usually result increased efficiency or payment.

Software tools and platforms in Digital Pathology: a review for clinicians and computer scientists

At the end of the twentieth century, a new technology was developed that allowed an entire tissue section to be scanned on an objective slide. Originally called virtual microscopy, this technology is now known as Whole Slide Imaging (WSI). WSI presents new challenges for reading, visualization, storage, and analysis. For this reason, several technologies have been developed to facilitate the handling of these images. In this paper, we analyze the most widely used technologies in the field of digital pathology, ranging from specialized libraries for the reading of these images to complete platforms that allow reading, visualization, and analysis. Our aim is to provide the reader, whether a pathologist or a computational scientist, with the knowledge to choose the technologies to use for new studies, development, or research.

Increasing a microscope's effective field of view via overlapped imaging and machine learning

This work demonstrates a multi-lens microscopic imaging system that overlaps multiple independent fields of view on a single sensor for high-efficiency automated specimen analysis. Automatic detection, classification and counting of various morphological features of interest is now a crucial component of both biomedical research and disease diagnosis. While convolutional neural networks (CNNs) have dramatically improved the accuracy of counting cells and sub-cellular features from acquired digital image data, the overall throughput is still typically hindered by the limited space-bandwidth product (SBP) of conventional microscopes. Here, we show both in simulation and experiment that overlapped imaging and co-designed analysis software can achieve accurate detection of diagnostically-relevant features for several applications, including counting of white blood cells and the malaria parasite, leading to multi-fold increase in detection and processing throughput with minimal reduction in accuracy.

Whole Slide Imaging (WSI) in Pathology: Current Perspectives and Future Directions

Whole slide imaging (WSI), ever since its first introduction about two decades ago, has been validated for a number of applications in the field of pathology. The recent approval of US FDA to a WSI system for use in primary surgical pathology diagnosis has opened avenues for wider acceptance and application of this technology in routine practice. The ongoing technological advances in digital scanners, image visualization methods, and the integration of artificial intelligence-derived algorithms with these systems provide opportunities of its newer applications. Its benefits are innumerable such as ease of access through internet, avoidance of physical storage space, and no risk of deterioration of staining quality or breakage of slides to name a few. Various barriers such as the high cost, technical glitches, and professional hesitation to adopt a new technology have hindered its use in pathology. This review article summarizes the technical aspects of WSI, its applications in diagnostic pathology, training, and research along with future perspectives. It highlights the benefits, limitations, and challenges delaying the use of this technology in routine practice. The review is targeted at students, residents, and budding pathologists to better acquaint them with the key aspects of state-of-the-art technology and enable them to implement WSI judiciously.

Recent technical advances in whole slide imaging instrumentation

Microscopic observation of biological specimen smears is the mainstay of diagnostic pathology, as defined by the Digital Pathology Association. Though automated systems for this are commercially available, their bulky size and high cost renders them unusable for remote areas. The research community is investing much effort towards building equivalent but portable, low-cost systems. An overview of such research is presented here, including a comparative analysis of recent reports. This paper also reviews recently reported systems for automated staining and smear formation, including microfluidic devices; and optical and computational automated microscopy systems including smartphone-based devices. Image pre-processing and analysis methods for automated diagnosis are also briefly discussed. It concludes with a set of foreseeable research directions that could lead to affordable, integrated and accurate whole slide imaging systems.

Design of embedded acoustic image acquisition system for wireless sensor network

In recent years, with the development of communication technology, embedded computing technology and sensor technology, it has become increasingly mature. Micro sensors with sensing, computing and communication capabilities have appeared in large numbers and developed rapidly, making wireless sensor networks widely used. People put forward higher requirements for the accuracy, reliability and flexibility of the image acquisition system. The image transmission system using analog technology not only has low image quality, but also has a serious waste of system resources, is not easy to form a complex network structure, and has poor functional scalability. In view of the actual needs of the current image acquisition and wireless transmission system, based on embedded technology, image acquisition, processing technology and network transmission technology, this paper proposes and designs a low-cost, high-reliability embedded image acquisition and wireless transmission system. Experimental tests show that this system has reasonable design, high video coding efficiency, good image continuity, stable operation, and basically realizes the display, storage and playback functions of the collected video data. Improve the transmission rate of the system and reduce the distortion caused by compression in terms of image compression. At the same time, it supports multiple image resolutions, frame rate options and multiple video formats, and the system’s transmission rate can adapt to the state of the network. This design fulfills the basic requirements of an embedded image acquisition system based on network technology, and provides a good foundation for the next development of a gigabit network-based image acquisition system.

Digital Microscopy, Image Analysis, and Virtual Slide Repository

Advancements in technology and digitization have ushered in novel ways of enhancing tissue-based research via digital microscopy and image analysis. Whole slide imaging scanners enable digitization of histology slides to be stored in virtual slide repositories and to be viewed via computers instead of microscopes. Easier and faster sharing of histologic images for teaching and consultation, improved storage and preservation of quality of stained slides, and annotation of features of interest in the digital slides are just a few of the advantages of this technology. Combined with the development of software for digital image analysis, digital slides further pave the way for the development of tools that extract quantitative data from tissue-based studies. This review introduces digital microscopy and pathology, and addresses technical and scientific considerations in slide scanning, quantitative image analysis, and slide repositories. It also highlights the current state of the technology and factors that need to be taken into account to insure optimal utility, including preanalytical considerations and the importance of involving a pathologist in all major steps along the digital microscopy and pathology workflow.

A Practical Guide to Whole Slide Imaging: A White Paper From the Digital Pathology Association

Context.—

Whole slide imaging (WSI) represents a paradigm shift in pathology, serving as a necessary first step for a wide array of digital tools to enter the field. Its basic function is to digitize glass slides, but its impact on pathology workflows, reproducibility, dissemination of educational material, expansion of service to underprivileged areas, and intrainstitutional and interinstitutional collaboration exemplifies a significant innovative movement with far-reaching effects. Although the benefits of WSI to pathology practices, academic centers, and research institutions are many, the complexities of implementation remain an obstacle to widespread adoption. In the wake of the first regulatory clearance of WSI for primary diagnosis in the United States, some barriers to adoption have fallen. Nevertheless, implementation of WSI remains a difficult prospect for many institutions, especially those with stakeholders unfamiliar with the technologies necessary to implement a system or who cannot effectively communicate to executive leadership and sponsors the benefits of a technology that may lack clear and immediate reimbursement opportunity.

Objectives.—

To present an overview of WSI technology—present and future—and to demonstrate several immediate applications of WSI that support pathology practice, medical education, research, and collaboration.

Data Sources.—

Peer-reviewed literature was reviewed by pathologists, scientists, and technologists who have practical knowledge of and experience with WSI.

Conclusions.—

Implementation of WSI is a multifaceted and inherently multidisciplinary endeavor requiring contributions from pathologists, technologists, and executive leadership. Improved understanding of the current challenges to implementation, as well as the benefits and successes of the technology, can help prospective users identify the best path for success.

Implementation of a real-time reference and calibration grid platform for improved screening - mapping in Pap test slides

Cervical cancer screening based on the Papanicolaou (Pap) test is a widely applied but not always efficient practice for detecting Human Papillomavirus (HPV) mediated lesions, partially due to a non-systematic and inadequate screening process. Our aim was to introduce an inexpensive easy-to-use direct screening platform for improved detection of abnormal cells indicative of underlying cervical neoplasia as well as persisting HPV infection. By employing a novel, efficient technique of laser-based micromachining, we achieved the fabrication of spatial grids on commercially available coverslips allowing visual segmentation of the slide for efficient screening. Abnormal and formerly diagnosed as negative for intraepithelial lesion or malignancy (NILM) Pap test slides (n = 200) were analyzed by conventional and grid-based screening. Grid-based microscopy led to a more reliable diagnosis compared to the conventional by identifying an increased number of abnormal cells (P = 0.001). It decreased borderline ASCUS, AGC diagnosis, increasing LSIL, HSIL and in situ AdenoCa detection rates closely related with biopsy (P = 0.015; kappa = 0.978). Concerning the set of NILM diagnoses in rapid re-screening, the method upgraded six cases (n = 6) to LSIL (P = 0.001). The proposed technical solution offers a calibration and orientation visual aid during the on-site screening process providing significant advantages compared to expensive digital imaging techniques.

An automated imaging system for radiation biodosimetry

We describe here an automated imaging system developed at the Center for High Throughput Minimally Invasive Radiation Biodosimetry. The imaging system is built around a fast, sensitive sCMOS camera and rapid switchable LED light source. It features complete automation of all the steps of the imaging process and contains built-in feedback loops to ensure proper operation. The imaging system is intended as a back end to the RABiT-a robotic platform for radiation biodosimetry. It is intended to automate image acquisition and analysis for four biodosimetry assays for which we have developed automated protocols: The Cytokinesis Blocked Micronucleus assay, the γ-H2AX assay, the Dicentric assay (using PNA or FISH probes) and the RABiT-BAND assay.