The importance of optical optimization in whole slide imaging (WSI) and digital pathology imaging

In the last 10 years, whole slide imaging (WSI) has seen impressive progress not only in image quality and scanning speed but also in the variety of systems available to pathologists. However, we have noticed that most systems have relatively simple optics axes and rely on software to optimize image quality and colour balance. While much can be done in software, this study examines the importance of optics, in particular optical filters, in WSI.Optical resolution is a function of the wavelength of light used and the numerical aperture of the lens system (Resolution = (f) wavelength/2 NA). When illumining light is not conditioned correctly with filters, there is a tendency for the wavelength to shift to longer values (more red) because of the characteristics of the lamps in common use. Most microscopes (but remarkably few WSI devices) correct for this with ND filter for brightness and Blue filter (depends on the light source) for colour correction.Using H&E slides research microscopes (Axiophot, Carl Zeiss MicroImaging, Inc. NY. Eclipse 50i., Nikon Inc. NY) at 20x, an attached digital camera (SPOT RT741 Slider Color, Diagnosis Instruments., MI USA), and a filter set, we examined the effect of filters and software enhancement on digital image quality. The focus value (as evaluated by focus evaluation software developed in house and SPOT imaging Software v4.6) was used as a proxy for image quality. Resolution of tissue features was best with the use of both the Blue and ND filters (in addition to software enhancement). Images without filters but with software enhancement while superficially good, lacked some details of specimen morphology and were unclear compared with the images with filters.The results indicate that the appropriate use of optical filters could measurably improve the appearance and resolution of WSI images.     

Weakly supervised learning and interpretability for endometrial whole slide image diagnosis

Fully supervised learning for whole slide image–based diagnostic tasks in histopathology is problematic due to the requirement for costly and time-consuming manual annotation by experts. Weakly supervised learning that utilizes only slide-level labels during training is becoming more widespread as it relieves this burden, but has not yet been applied to endometrial whole slide images, in iSyntax format. In this work, we apply a weakly supervised learning algorithm to a real-world dataset of this type for the first time, with over 85% validation accuracy and over 87% test accuracy. We then employ interpretability methods including attention heatmapping, feature visualization, and a novel end-to-end saliency-mapping approach to identify distinct morphologies learned by the model and build an understanding of its behavior. These interpretability methods, alongside consultation with expert pathologists, allow us to make comparisons between machine-learned knowledge and consensus in the field. This work contributes to the state of the art by demonstrating a robust practical application of weakly supervised learning on a real-world digital pathology dataset and shows the importance of fine-grained interpretability to support understanding and evaluation of model performance in this high-stakes use case.     

Accuracy of a remote quantitative image analysis in the whole slide images

The rationale for choosing a remote quantitative method supporting a diagnostic decision requires some empirical studies and knowledge on scenarios including valid telepathology standards. The tumours of the central nervous system [CNS] are graded on the base of the morphological features and the Ki-67 labelling Index [Ki-67 LI]. Various methods have been applied for Ki-67 LI estimation. Recently we have introduced the Computerized Analysis of Medical Images [CAMI] software for an automated Ki-67 LI counting in the digital images. Aims of our study was to explore the accuracy and reliability of a remote assessment of Ki-67 LI with CAMI software applied to the whole slide images [WSI]. The WSI representing CNS tumours: 18 meningiomas and 10 oligodendrogliomas were stored on the server of the Warsaw University of Technology. The digital copies of entire glass slides were created automatically by the Aperio ScanScope CS with objective 20x or 40x. Aperio's Image Scope software provided functionality for a remote viewing of WSI. The Ki-67 LI assessment was carried on within 2 out of 20 selected fields of view (objective 40x) representing the highest labelling areas in each WSI. The Ki-67 LI counting was performed by 3 various methods: 1) the manual reading in the light microscope - LM, 2) the automated counting with CAMI software on the digital images - DI , and 3) the remote quantitation on the WSIs - as WSI method. The quality of WSIs and technical efficiency of the on-line system were analysed. The comparative statistical analysis was performed for the results obtained by 3 methods of Ki-67 LI counting. The preliminary analysis showed that in 18% of WSI the results of Ki-67 LI differed from those obtained in other 2 methods of counting when the quality of the glass slides was below the standard range. The results of our investigations indicate that the remote automated Ki-67 LI analysis performed with the CAMI algorithm on the whole slide images of meningiomas and oligodendrogliomas could be successfully used as an alternative method to the manual reading as well as to the digital images quantitation with CAMI software. According to our observation a need of a remote supervision/consultation and training for the effective use of remote quantitative analysis of WSI is necessary.     

The relationship between cancer detection in mammography and image quality measurements

PurposeTo investigate the relationship between image quality measurements and the clinical performance of digital mammographic systems.MethodsMammograms containing subtle malignant non-calcification lesions and simulated malignant calcification clusters were adapted to appear as if acquired by four types of detector. Observers searched for suspicious lesions and gave these a malignancy score. Analysis was undertaken using jackknife alternative free-response receiver operating characteristics weighted figure of merit (FoM). Images of a CDMAM contrast-detail phantom were adapted to appear as if acquired using the same four detectors as the clinical images. The resultant threshold gold thicknesses were compared to the FoMs using a linear regression model and an F-test was used to find if the gradient of the relationship was significantly non-zero.ResultsThe detectors with the best image quality measurement also had the highest FoM values. The gradient of the inverse relationship between FoMs and threshold gold thickness for the 0.25 mm diameter disk was significantly different from zero for calcification clusters (p = 0.027), but not for non-calcification lesions (p = 0.11). Systems performing just above the minimum image quality level set in the European Guidelines for Quality Assurance in Breast Cancer Screening and Diagnosis resulted in reduced cancer detection rates compared to systems performing at the achievable level.ConclusionsThe clinical effectiveness of mammography for the task of detecting calcification clusters was found to be linked to image quality assessment using the CDMAM phantom. The European Guidelines should be reviewed as the current minimum image quality standards may be too low.     

Current state of whole slide imaging use in cytopathology: Pros and pitfalls

Whole slide imaging (WSI) allows generation of large whole slide images and their navigation with zoom in and out like a true virtual microscope. It has become widely used in surgical pathology for many purposes, such as education and training, research activity, teleconsultation, and primary diagnosis. However, in cytopathology, the use of WSI has been lagging behind histology, mainly due to the cytological specimen's characteristics, as groups of cells of different thickness are distributed throughout the slide. To allow the same focusing capability of light microscope, slides have to be scanned at multiple focal planes, at the cost of longer scan times and larger file size. These are the main technical pitfalls of WSI for cytopathology, partly overcome by solutions like liquid‐based preparations. Validation studies for the use in primary diagnosis are less numerous and more heterogeneous than in surgical pathology. WSI has been proved effective for training students and successfully used in proficiency testing, allowing the creation of digital cytology atlases. Longer scan times are also a barrier for use in rapid on‐site evaluation, but WSI retains its advantages of easy sharing of images for consultation, multiple simultaneous viewing in different locations, the possibility of unlimited annotations and easy integration with medical records. Moreover, digital slides set the laboratory free from reliance on a physical glass slide, with no more concern of fading of stain or slide breakage. Costs are still a problem for small institutions, but WSI can also represent the beginning of a more efficient way of working.     

High throughput slanted scanning whole slide imaging system for digital pathology

In whole slide imaging (WSI), normally only a one layer imaging of the slide is performed. Autofocus at multiple positions is usually required. But defocus blur still exists due to tissue folding or specimen thickness. Repeated Z-stack scan be applied here, which, however, is too time consuming. Here, a high throughput slanted scanning WSI system is reported. In this system, the slide surface was slanted 1° relative to the focal plane. Thus, the focal plane spanned multiple layers of the sample. By moving the slide, multi-layer image data of the sample can be acquired simultaneously at a time frame comparable to conventional 1-layer imaging. With image fusion, defocus blur can be avoided. High quality and fast imaging of both cytological and histological slide specimens was demonstrated without applying aberration correction. The system can be a highly efficient way for the application of WSI in digital pathology.     

Color standardization method and system for whole slide imaging based on spectral sensing

In the field of whole slide imaging, the imaging device or staining process cause color variations for each slide that affect the result of image analysis made by pathologist. In order to stabilize the analysis, we developed a color standardization method and system as described below. (1) Color standardization method based on RGB imaging and multi spectral sensing, which utilize less band (16 bands) than conventional method (60 bands). (2) High speed spectral sensing module. As a result, we confirmed the following effect. (1) We confirmed the performance improvement of nucleus detection by the color standardization. And we can conduct without training data set which is needed in conventional method. (2) We can get detection performance of H&E component equivalent to conventional method (60 bands). And measurement process is more than 255 times faster.     

Distributed computing in image analysis using open source frameworks and application to image sharpness assessment of histological whole slide images

Background

Automated image analysis on virtual slides is evolving rapidly and will play an important role in the future of digital pathology. Due to the image size, the computational cost of processing whole slide images (WSIs) in full resolution is immense. Moreover, image analysis requires well focused images in high magnification.

Methods

We present a system that merges virtual microscopy techniques, open source image analysis software, and distributed parallel processing. We have integrated the parallel processing framework JPPF, so batch processing can be performed distributed and in parallel. All resulting meta data and image data are collected and merged. As an example the system is applied to the specific task of image sharpness assessment. ImageJ is an open source image editing and processing framework developed at the NIH having a large user community that contributes image processing algorithms wrapped as plug-ins in a wide field of life science applications. We developed an ImageJ plug-in that supports both basic interactive virtual microscope and batch processing functionality. For the application of sharpness inspection we employ an approach with non-overlapping tiles. Compute nodes retrieve image tiles of moderate size from the streaming server and compute the focus measure. Each tile is divided into small sub images to calculate an edge based sharpness criterion which is used for classification. The results are aggregated in a sharpness map.

Results

Based on the system we calculate a sharpness measure and classify virtual slides into one of the following categories - excellent, okay, review and defective. Generating a scaled sharpness map enables the user to evaluate sharpness of WSIs and shows overall quality at a glance thus reducing tedious assessment work.

Conclusions

Using sharpness assessment as an example, the introduced system can be used to process, analyze and parallelize analysis of whole slide images based on open source software.

     

The Yorkshire slide exchange external quality assessment (EQA) scheme

A slide circulation scheme measuring cervical screening performance of individual cytologists in 15 laboratories in Yorkshire Regional Health Authority is described. The advantages and disadvantages are compared with the current National Proficiency Testing (NPT) scheme. The results indicate that a slide circulation scheme can be successfully used in cervical cytology external quality assessment (EQA). Levels of participation are better than those currently achieved by regional variations of the NPT scheme, and the use of laboratory consensus in the selection of scoring slides appears to be no less valid than the use of a pre‐selected slide pool assembled by an expert panel. The volume of data accumulated in one round is considerably greater than that achieved by proficiency testing and the educational value is regarded as high. However, the scheme is very time consuming for participants and consequently expensive for laboratories. The lack of external supervision increases the risk of unfair practices within individual laboratories. Because of these problems, Yorkshire has now switched to an NPT scheme.     

A relationship between wool quality and blood potassium type in sneep

Fibre diameter and medullation percentage in the wool of 474 adult ewes of 3 breeds, belonging to high (HK) and low (LK) blood potassium type have been determined (Marwari 78 LK/198 HK; Chokla 42 LK/56 HK and Russian Merino × Marwari 66 LK/34 HK). No significant difference between potassium types within any of the breeds was observed in medullation percentage. While no significant relationship between potassium type and fibre diameter was observed in individual breeds, least square analysis of the pooled data for the three breeds indicated that there is a possibility of such an association approaching significance, the LK type animal having the potentiality of yielding finer wool than the HK.     

Reconciliation and relationship quality in Assamese macaques (Macaca assamensis)

A consistent conclusion in reconciliation research is that animals that reconcile are likely to have strong social bonds. This has led to the hypothesis that reconciliation occurs most often between valuable social partners. We tested this hypothesis in a group of Assamese macaques (Macaca assamensis) living near a temple in Assam, India. Using focal sample and ad libitum data collection, we recorded the occurrence of reconciliation, grooming, and agonistic aiding, and the outcomes of approach. We used matrix association methods (TauKr correlation) to correlate reconciliation with grooming, aiding, and approach outcome. Females reconciled more often with females with which they had stronger grooming and aiding relationships. The correlation between reconciliation and aiding was significant for support to the aggressor and the victim. In contrast, no such correlations with reconciliation were found for males. This study provides evidence that females reconcile most often with valuable and compatible social partners. The results do not support the relationship-quality hypothesis for males, and we suggest that future studies give more consideration to the possibility that males reconcile for reasons other than to repair relationships with valuable partners.     

宽恕与睡眠质量关系的研究进展

近年来,国内外对宽恕的研究逐渐增多,但宽恕与睡眠质量关系的研究较少,本文通过综述现有的一些研究资料,分析二者之间的关系。分析表明,人际侵犯事件是影响宽恕的外部因素,其严重程度直接影响受害者的宽恕水平及睡眠质量;宽恕能够降低受害者的生理唤醒、情绪唤醒、及认知唤醒,从而改善睡眠质量,但之间的相互作用及具体的内在影响机制并不明确。同时,影响宽恕水平的宜人性、外倾等人格特质也会影响睡眠质量。最后分析了目前研究中存在的缺陷,并对宽恕与睡眠质量关系的研究前景进行了展望。     

宽恕与睡眠质量关系的研究进展

近年来,国内外对宽恕的研究逐渐增多,但宽恕与睡眠质量关系的研究较少,本文通过综述现有的一些研究资料,分析二者之间的关系。分析表明,人际侵犯事件是影响宽恕的外部因素,其严重程度直接影响受害者的宽恕水平及睡眠质量;宽恕能够降低受害者的生理唤醒、情绪唤醒、及认知唤醒,从而改善睡眠质量,但之间的相互作用及具体的内在影响机制并不明确。同时,影响宽恕水平的宜人性、外倾等人格特质也会影响睡眠质量。最后分析了目前研究中存在的缺陷,并对宽恕与睡眠质量关系的研究前景进行了展望。