Preserving and sharing examples of anatomical variation and developmental anomalies via photorealistic virtual reality

Computer graphics technology has made it possible to create photographic-quality virtual specimens from real anatomical material. One technique for doing this, QuickTime Virtual Reality (QTVR), results in virtual specimens that are easily shared on the Internet and displayed as standalone entities or incorporated into complex programs or Web sites. A compelling use of this technology is the sharing of rare specimens such as unusual variations, developmental anomalies or gross pathology. These types of specimens have traditionally been confined to anatomical museums, but could serve a much more useful existence as freely shared virtual specimens. An example presented here is a relatively rare developmental defect in the embryonic aortic arches that results in a right-sided aortic arch coursing posterior to the trachea and esophagus. In a time of ever increasing restraints on the practical side of anatomy education, an Internet-based library of human variation and other rare specimens would be a useful supplement to students' limited exposure to the human body. Since the discovery and preparation of specimens would be the rate-limiting step in producing such a collection, we propose the establishment of a center for virtual specimen creation and preservation through a cooperative effort by gross anatomists and pathologists in contributing the source material. This collection, a work in progress, is available at www.anatomy.wright.edu/qtvr.     

High-performance computing, high-speed networks, and configurable computing environments: progress toward fully distributed computing.

The next several years will see the maturing of a collection of technologies that will enable fully and transparently distributed computing environments. Networks will be used to configure independent computing, storage, and I/O elements into "virtual systems" that are optimal for solving a particular problem. This environment will make the most powerful computing systems those that are logically assembled from network-based components and will also make those systems available to a widespread audience. Anticipating that the necessary technology and communications infrastructure will be available in the next 3 to 5 years, we are developing and demonstrating prototype applications that test and exercise the currently available elements of this configurable environment. The Lawrence Berkeley Laboratory (LBL) Information and Computing Sciences and Research Medicine Divisions have collaborated with the Pittsburgh Supercomputer Center to demonstrate one distributed application that illuminates the issues and potential of using networks to configure virtual systems. This application allows the interactive visualization of large three-dimensional (3D) scalar fields (voxel data sets) by using a network-based configuration of heterogeneous supercomputers and workstations. The specific test case is visualization of 3D magnetic resonance imaging (MRI) data. The virtual system architecture consists of a Connection Machine-2 (CM-2) that performs surface reconstruction from the voxel data, a Cray Y-MP that renders the resulting geometric data into an image, and a workstation that provides the display of the image and the user interface for specifying the parameters for the geometry generation and 3D viewing. These three elements are configured into a virtual system by using several different network technologies. This paper reviews the current status of the software, hardware, and communications technologies that are needed to enable this configurable environment. These interdependent technologies include: (1) user interface and application program construction methodologies, (2) the interprocess communication (IPC) mechanisms used to connect the software modules of the application, (3) the network protocols and interface hardware used by the IPC for communicating between modules running on separate and independent computing system elements, (4) the telecommunications infrastructure that provides the low-level data transfer functions for the networks that connect the geographically distributed elements used by the application, and (5) the nature of the functional elements that will be connected to form virtual systems.     

Automated MECOS-Ts2 microscopy complex in pathologoanatomic practice

Computer-aided and information systems of a MECOS-Ts2 microscopy complex designed to transmit a representative image of a specimen along communication lines are considered. The above systems allow the use of the complex: 1) in on-line and off-line modes to provide tele-medical services (cytology, histology, etc.); moreover, the requirements for channel traffic may be decreased over and over again as compared to the routine on-line videomicroscopy mode; 2) for telemedical tests of specialized local automatic procedures of microscopical analysis (analysis of smears of blood and bone-marrow smears, parasitological analysis, etc.); 3) for collection of a representative electronic archive of the "virtual" specimens of rare nosological entities, which have been obtained in different medical institutions, w hich will provide valid statistical assessments of diagnostic decisions; 4) for remote accompaniment of MECOS-Ts2 complexes by the manufacture (update of versions, training, quality control of sample preparation, collection of commission statistics); 5) for training and certification of remote laboratory staff. The functions considered cannot be implemented in analyzers of other types, in flow analyzers, in particular.     

Digital photography in anatomical pathology

Digital imaging has made major inroads into the routine practice of anatomical pathology and replaces photographic prints and Kodachromes for reporting and conference purposes. More advanced systems coupled to computers allow greater versatility and speed of turnaround as well as lower costs of incorporating macroscopic and microscopic pictures into pathology reports and publications. Digital images allow transmission to remote sites via the Internet for consultation, quality assurance and educational purposes, and can be stored on and disseminated by CD-ROM. Total slide digitisation is now a reality and will replace glass slides to a large extent. Three-dimensional images of gross specimens can be assembled and posted on websites for interactive educational programmes. There are also applications in research, allowing more objective and automated quantitation of a variety of morphological and immunohistological parameters. Early reports indicate that medical vision systems are a reality and can provide for automated computer-generated histopathological diagnosis and quality assurance.     

Virtual microscopy and routine diagnostics. A discussion paper

There are several areas of application for virtual microscopy in pathology. After broad use in education and research, we are now seeing its initial application in health care. We can predict that, on the basis of experience gained in digital radiology and early experience in pathology, VM will be established as routine. However, its introduction will follow a different course to that taken in digital radiology, which required that the computer be accepted as a "necessary evil" to record and display computer tomograms. Virtual microscopy needs to ensure that it supports the pathologist significantly in terms of access to archives, quantification of markers, display of biopsy stacks, cooperation with colleagues, etc. Consequently, the question of "When will virtual microscopy enter daily pathology practice?" may not only be answered on the basis of technical features. Of course, it is necessary that scanning speed goes below 1 min/cm(2) and that it remains financially viable, but more important is an optimal integration of virtual microscopy in daily pathology routine. This process will extend over several decades, as past developments in digital radiology have shown.     

Utility of whole slide imaging and virtual microscopy in prostate pathology

Whole slide imaging (WSI) has been used in conjunction with virtual microscopy (VM) for training or proficiency testing purposes, multicentre research, remote frozen section diagnosis and to seek specialist second opinion in a number of organ systems. The feasibility of using WSI/VM for routine surgical pathology reporting has also been explored. In this review, we discuss the utility and limitations of WSI/VM technology in the histological assessment of specimens from the prostate. Features of WSI/VM that are particularly well suited to assessment of prostate pathology include the ability to examine images at different magnifications as well as to view histology and immunohistochemistry side-by-side on the screen. Use of WSI/VM would also solve the difficulty in obtaining multiple identical copies of small lesions in prostate biopsies for teaching and proficiency testing. It would also permit annotation of the virtual slides, and has been used in a study of inter-observer variation of Gleason grading to facilitate precise identification of the foci on which grading decisions had been based. However, the large number of sections examined from each set of prostate biopsies would greatly increase time required for scanning as well as the size of the digital file, and would also be an issue if digital archiving of prostate biopsies is contemplated. Z-scanning of glass slides, a process that increases scanning time and file size would be required to permit focusing a virtual slide up and down to assess subtle nuclear features such as nucleolar prominence. The common use of large blocks to process prostatectomy specimens would also be an issue, as few currently available scanners can scan such blocks. A major component of proficiency testing of prostate biopsy assessment involves screening of the cores to detect small atypical foci. However, screening virtual slides of wavy fragmented prostate cores using a computer mouse aided by an overview image is very different from screening glass slides using a microscope stage. Hence, it may be more appropriate in this setting to mark the lesional area and focus only on the interpretation component of competency testing. Other issues limiting the use of digital pathology in prostate pathology include the cost of high quality slide scanners for WSI and high resolution monitors for VM as well as the requirement for fast Internet connection as even a subtle delay in presentation of images on the screen may be very disturbing for a pathologist used to the rapid viewing of glass slides under a microscope. However, these problems are likely to be overcome by technological advances in the future.     

The use of virtual reality in assessment and treatment of anxiety and related disorders

In recent years the development of new virtual environments has been qualitatively high and fast at the same time, but the dissemination of virtual reality (VR) in clinical practice is still scarce. The aim of this review is to give an insight into the state of the art of the use of VR as an assessment tool and treatment intervention in anxiety and related disorders as posttraumatic stress disorder and obsessive–compulsive disorders. Besides an overview into the efficacy of VR, a summary will be given on assumed working mechanisms in virtual reality exposure therapy and how this aligns with current theoretical models. Further, it will be discussed how VR is accepted by patients and research into the reluctance of therapist to use this technology during treatment with focus on the therapeutic alliance and how it may be influenced by the use of VR. Finally, we discuss clinical and future issues as, for example, dissemination into clinical practice and what VR has to offer therapists in future. This not only in adult population but as well in younger patients, as young adolescents VR has a great potential as it connects easily with its playful elements to this population and might be a low threshold step to offer treatment or preventive interventions.     

Digital slide and virtual microscopy based routine and telepathology evaluation of routine gastrointestinal biopsy specimens

AIMS: To evaluate a recently developed digital slide and virtual microscope system, and to compare this method with optical microscopy on routine gastrointestinal biopsy specimens in both local and remote access modes. METHODS: A fully computer controlled commercial microscope was used. The scanning program included object detection, autofocus, and image compression algorithms. The overall hard disk space for a gastric biopsy was between 30 and 50 MB and the scanning time was between 20 and 40 minutes. Haematoxylin and eosin stained routine gastric (61) and colon (42) biopsy specimens were selected, scanned, and evaluated by two specialists on an optical (OM) and virtual microscope (VM). RESULTS: The overall concordance of VM and OM with the consensus diagnosis was 95.1% and 97%, respectively. Clinically important concordance was 96.1% and 98% for VM and OM, respectively. The two methods showed concordance in 92% of cases and clinically important concordance in 94.1% of cases. The reasons for discordance were image quality (one case), interpretation difference (three cases), and insufficient clinical information (three cases). Remote evaluation of the digital slides through the Internet has the advantages of the previously used static and dynamic telepathology methods. CONCLUSIONS: Diagnostic concordance was found between OM and VM. The digital slide and the virtual microscope can be alternative techniques in the computerisation of the histology laboratory and in teleconsultation services after further evaluation of time and storage constraints.     

Feasibility of a molecular screening method for detection of Salmonella enterica and Campylobacter jejuni in a routine community-based clinical microbiology laboratory

Conventional diagnostic methods for the detection of Salmonella enterica and Campylobacter jejuni are laborious and time-consuming procedures, resulting in final results, for the majority of specimens, only after 3 to 4 days. Molecular detection can improve the time to reporting of the final results from several days to the next day. However, molecular assays for the detection of gastrointestinal pathogens directly from stool specimens have not made it into the routine clinical microbiology laboratory. In this study we have assessed the feasibility of a real-time PCR-based molecular screening method (MSM), aimed at S. enterica and C. jejuni, in the daily practice of a routine clinical microbiology laboratory. We have prospectively analyzed 2,067 stool specimens submitted for routine detection of gastrointestinal bacterial pathogens over a 7-month period. The MSM showed 98 to 100% sensitivity but routine culture showed only 77.8 to 86.8% sensitivity when an extended "gold standard" that included all culture-positive and all MSM-positive specimens, as confirmed by an independent secondary PCR of a different target gene, was used. An overall improvement in the rate of detection of both pathogens of 15 to 18% was observed. Both approaches performed nearly identically with regard to the specificity, positive predictive value, and negative predictive value, with the values for MSM being 99.7%, 93.1 to 96.6%, and 99.8 to 100%, respectively, and those for routine culture being 100%, 100%, and 97.6 to 99.5%, respectively. Finally, the final results were reported between 3 and 4 days earlier for negative specimens compared to the time of reporting of the results of routine culture. Positive specimens, on the other hand, required an additional 2 days to obtain a final result compared to the time required for routine culture, although preliminary MSM PCR-positive results were reported, on average, 2.9 to 3.8 days before the final routine culture results were reported. In conclusion, MSM can be incorporated into the daily practice of a routine clinical microbiology laboratory with ease. Furthermore, it provides an improvement in the screening for S. enterica and C. jejuni and substantially improves the time to the reporting of negative results.     

Virtual microscopy: an evaluation of its validity and diagnostic performance in routine histologic diagnosis of skin tumors

Digitization of histologic slides is associated with many advantages, and its use in routine diagnosis holds great promise. Nevertheless, few articles evaluate virtual microscopy in routine settings. This study is an evaluation of the validity and diagnostic performance of virtual microscopy in routine histologic diagnosis of skin tumors. Our aim is to investigate whether conventional microscopy of skin tumors can be replaced by virtual microscopy. Ninety-six skin tumors and skin-tumor–like changes were consecutively gathered over a 1-week period. Specimens were routinely processed, and digital slides were captured on Mirax Scan (Carl Zeiss MicroImaging, Göttingen, Germany). Four pathologists evaluated the 96 virtual slides and the associated 96 conventional slides twice with intermediate time intervals of at least 3 weeks. Virtual slides that caused difficulties were reevaluated to identify possible reasons for this. The accuracy was 89.2% for virtual microscopy and 92.7% for conventional microscopy. All κ coefficients expressed very good intra- and interobserver agreement. The sensitivities were 85.7% (78.0%-91.0%) and 92.0% (85.5%-95.7%) for virtual and conventional microscopy, respectively. The difference between the sensitivities was 6.3% (0.8%-12.6%). The subsequent reevaluation showed that virtual slides were as useful as conventional slides when rendering a diagnosis. Differences seen are presumed to be due to the pathologists' lack of experience using the virtual microscope. We conclude that it is feasible to make histologic diagnosis on the skin tumor types represented in this study using virtual microscopy after pathologists have completed a period of training. Larger studies should be conducted to verify whether virtual microscopy can replace conventional microscopy in routine practice.     

Comparison of the Lumac and Monolight systems for detection of bacteriuria by bioluminescence

The development of practical and rapid methods for detection of infectious-disease-producing agents in clinical specimens is the most important current goal of clinical microbiology. Bioluminescence is a technique which is rapid and potentially sensitive enough to detect significant numbers of bacteria in urine specimens. To determine whether bioluminescence is practical and cost effective for routine use, we compared two commercially available instruments and kits, Lumac and Monolight, to standard bacterial cultures on 986 urine specimens. Lumac had an overall 83.7% agreement with cultures, a sensitivity of 92.4%, and a specificity of 79.4%. Monolight had 83.5% agreement with cultures, a sensitivity of 89.1%, and a specificity of 81.8%. There were 13.8% false-positive results and 2.5% false-negative results with both systems. When only potentially significant organisms were included, the false-negative rate was reduced to ca. 1%. Both systems are sufficiently accurate to be recommended for routine use. The cost of bioluminescence is higher than that of bacterial cultures, and bioluminescence may not be cost effective in some laboratories.     

Aseptic meningitis and encephalitis: the role of PCR in the diagnostic laboratory.

In this study we have devised a simple and robust PCR strategy to detect a wide range of viruses, bacteria, and parasites, all of which are capable of causing aseptic meningitis and encephalitis. The techniques developed have been used in a routine diagnostic virology laboratory to test prospectively 2,233 cerebrospinal fluid specimens. A virus was detected in 147 specimens of cerebrospinal fluid from 143 patients. Four sets of primers were sufficient to detect the virus in 135 (94%) of the PCR-positive patients. We conclude that with appropriate primers, PCR can be systematically and economically applied to test for a range of organisms in a routine diagnostic laboratory. In our opinion, PCR will soon become the "gold standard" test for viral infections of the central nervous system.     

Depositing archived paraffin tissue core biopsy specimens in paraffin tissue microarrays using a paraffin tissue punch modified with a countersink

Paraffin tissue microarrays (PTMAs) introduced by Kononen et al in 1998 have become a widely used technique in routine pathology and even more so in research. Kononen used a tissue puncher/arrayer (Beecher Instruments, Sun Prairie, WI, USA) to take paraffin tissue core biopsy specimens (PTCBs) of 0.6-2 mm in diameter from routine paraffin tissue blocks and transfer them to another paraffin block with up to 1000 holes. As pointed out by Mengel et al, however, it is not possible to use the Kononen/Beecher system to construct PTMAs out of archived PTCBs. To overcome this drawback in the extremely popular Beecher system, the paraffin tissue punch was modified by incorporating a conical 4 mm deep countersink. This countersink was milled with a conical precision cutter that can be bought in an ordinary hardware store (cost <5 US dollars). The countersink facilitates the insertion of an archived PTCB into the paraffin tissue punch and enables the construction of PTMAs with previously archived PTCBs using the widely distributed Beecher system. Moreover, this paraffin tissue punch can be used for other systems to create PTMAs, such as the low-budget systems designed by Vogel.     

Rapid detection of Mycobacterium tuberculosis in various clinical specimens by using polymerase chain reaction combined with a nonradioactive hybridization system

A DNA amplification system using the polymerase chain reaction (PCR) combined with a nonradioactive digoxigenin-labeled probe hybridization was employed to detect Mycobacterium tuberculosis in clinical specimens. One hundred and thirty specimens were tested by several methods including routine culture method, acid-fast staining, BACTEC 460 detection system, PCR, and PCR-hybridization techniques. Sixteen out of 130 specimens were culture positive on Middlebrook 7H11 agar, 10 were positive with acid-fast staining, 18 were positive with BACTEC 460 detection system, 23 were positive with PCR technique, and 62 were positive with PCR-nonradioactive hybridization technique. When compared with culture results, PCR-nonradioactive hybridization had an overall sensitivity of 100% (16/16) and a specificity of 59.7% (68/114). However, 28 out of 46 (60.9%) PCR-nonradioactive hybridization positive specimens which were culture negative had clinical data supporting the diagnosis of tuberculosis. In addition, 4 specimens which were negative by routine culture but positive by BACTEC 460 detection system and two specimens which were negative by routine culture but positive by acid-fast staining were all positive by PCR-hybridization technique. These data suggest that routine culture method may not be sensitive enough to detect M. tuberculosis in all kinds of clinical specimens. Taking this deviation into account, the specificity of PCR-nonradioactive hybridization technique may be rectified range from 63% (68/108) to 79.1% (68/86). PCR itself is not satisfactory enough to detect M. tuberculosis in specimens (the sensitivity and specificity were 56.3% and 87.7%, respectively) in this study. However, when it combines with DNA hybridization technique, they can be a very powerful and rapid diagnostic tool to detect M. tuberculosis in clinical specimens.     

Virtual microscopy in systems pathology

Genomics and proteomics have evolved towards systems biology. The general goal here is the construction of complex, functional models of biological systems on the basis of molecular networks. Such models enable improved quality in interpretation and evaluation of quantitative measurements and afford a substantially deeper functional understanding. Systems pathology differs from systems biology by attaching the same importance to spatial modelling of tissue alterations as to gene regulatory modelling. In this way, systems pathology is able to deploy disease models for improved diagnosis, prognosis and therapy. In the present work a generic process for systems pathology is created, integrating gene regulatory and morphological models towards molecular disease models. For this purpose, fluorescent virtual microscopy will be essential as it delivers morphological and molecular tissue data with high spatial resolution and high throughput. Using epidermal differentiation as an example, it is shown how - using virtual microscopy - the spatiotemporal expression of biomarkers can be modelled by reconstructing protein networks from fluorescent tissue sections.     

Telepathology overview: From concept to implementation

Telepathology is the practice of pathology at a distance by using video imaging and telecommunications. Significant progress has been made in telepathology. To date, 12 classes of telepathology systems have been engineered. Rapid and ultrarapid virtual slide processors may further expand the range of telepathology applications. Next-generation digital imaging light microscopes, such as miniaturized microscope arrays (MMA), may make virtual slide processing a routine laboratory tool. Diagnostic accuracy of telepathology is comparable with that of conventional light microscopy for most diagnoses. Current telepathology applications include intraoperative frozen sections services, routine surgical pathology services, second opinions, and subspecialty consultations. Three telepathology practice models are discussed: the subspecialty practice (SSP) model; the case triage practice (CTP) model; and the virtual group practice (VGP) model. Human factors influence performance with telepathology. Experience with 500 telepathology cases from multiple organs significantly reduces the video viewing time per case (P < .01). Many technology innovations can be represented as S-curves. After long incubation periods, technology use and/or efficiency may accelerate. Telepathology appears to be following an S-curve for a technical innovation.     

Three-dimensional image and virtual dissection program of the brain made of Korean cadaver

The three-dimensional (3D) structure of the brain needs to be understood for accurate diagnosis and treatment of brain diseases. The brain of a cadaver may not always be available for dissection when it is needed. To overcome this problem, we attempted to create a 3D image and virtual dissection program of the brain using a Korean cadaver. The brain extracted from a Korean male cadaver was embedded in gelatin solution. 130 MRI of the brain were taken and 130 serially-sectioned specimens were made. All of MRI and specimens were inputted into the computer, and 10 brain components were manually segmented. A 3D image and virtual dissection program of the brain was made. Various virtual dissection functions were established, such as 1) sectioning the 3D image of the brain at free angles to represent its plane as a real image, segmented image, and MRI, 2) identifying the brain components represented in the sectioned plane, and 3) rotating the 3D image of the whole brain or the selected brain components at free angles. The resulting virtual dissection program of the brain is helpful in better understanding the 3D location and shape of the brain components and it is expected to be used as a CD-title or through Internet as an educational tool for medical students and doctors.     

Diagnosis of varicella-zoster virus infections in the clinical laboratory by LightCycler PCR

Varicella-zoster virus (VZV) causes vesicular dermal lesions which are clinically evident as varicella (primary infection) or zoster (reactivated) diseases. The LightCycler system (Roche Molecular Biochemicals) is a newly developed commercially available system designed to rapidly perform PCR with real-time detection of PCR products using a fluorescence resonance energy transfer. We compared the detection of VZV from dermal specimens by shell vial cell culture (MRC-5) and by LightCycler PCR. Of 253 specimens, VZV was detected in 23 (9.1%) by shell vial cell cultures and 44 (17.4%) by LightCycler PCR directed to a nucleic acid target sequence in gene 28. Twenty-one of 44 (47.7%) specimens were exclusively positive by LightCycler PCR; the shell vial cell culture assay was never positive when DNA amplification was negative (specificity, 100%). VZV DNA was detected in 39 of 44 (88.6%) specimens positive during cycles 10 through 30 of the LightCycler PCR. These VZV DNA-positive specimens (cycles 10 to 30) and 5 of 11 other PCR positive specimens (cycles 31 to 36) were confirmed by another LightCycler PCR directed to another (gene 29) target of the viral genome. For routine laboratory practice, all specimens yielding amplified DNA to the VZV gene 28 target can be considered positive results. The increased sensitivity (91%) of the LightCycler PCR for detection of VZV, rapid turnaround time for reporting results, virtual elimination of amplicon carryover contamination, and equivalent costs compared to shell vial cell culture for detection of VZV indicate the need for implementation of this technology for routine laboratory diagnosis of this viral infection.     

Progression in diagnostic pathology; development of virtual microscopy and its applications

Many systems have already been designed and successfully used for clinical laboratory and pathological examination. The evolution of image analysis was enabled when analog images of the original glass slides could be transferred to digital images with the rapid development of virtual microscopy and virtual slides depended upon computer technologies. Today, whole slide can be acquired by virtual microscopes. The applications of virtual microscopy and virtual slides for teaching, diagnosis, telepathology, and research are more widely used than those of real microscope and real glass slides. In traditional cancer diagnosis, pathologists examine biopsies to make diagnostic assessments largely based on two-dimensional cell morphology and tissue distribution. These assessments are subjective and often show considerable variability. However, automated cancer diagnostic system based on three-dimensional image analysis based on nuclear bulging sign enables objective judgments using quantitative measurements. We expect that the shortage of pathologists will be improved when an automated cancer diagnosis system is developed.     

Current concepts in the classification of thoracic neuroendocrine tumours

Bronchopulmonary neuroendocrine tumours (NETs) share features with extrathoracic NETs and comprise a spectrum of neuroendocrine neoplasms, most of which are also mirrored by counterparts in the thymus. Accurate classification remains difficult on morphological criteria alone, as overlapping and transitional phenotypes occur and reproducibility of classification is marred by ambiguity, heterogeneity and sampling error, and artefacts, especially in cytology and small biopsy specimens. While there have been significant advances in the immunohistochemical and molecular characterization and phenotyping of thoracic NETs in recent years, and this holds great promise for the development of therapeutically relevant categories, this has not yet led to a shift in pathology practice. In this review, the current World Health Organization (WHO) classification of thoracic NETs will be discussed, areas of diagnostic difficulty highlighted, an overview of recent evidence for clinically relevant immunohistochemical and molecular phenotypes provided, and their potential for introduction into routine practice discussed.