Darren Treanor

A Nonlinear Mapping Approach to Stain Normalization in Digital Histopathology Images Using Image-Specific Color Deconvolution

Histopathology diagnosis is based on visual examination of the morphology of histological sections under a microscope. With the increasing popularity of digital slide scanners, decision support systems based on the analysis of digital pathology images are in high demand. However, computerized decision support systems are fraught with problems that stem from color variations in tissue appearance due to variation in tissue preparation, variation in stain reactivity from different manufacturers/batches, user or protocol variation, and the use of scanners from different manufacturers. In this paper, we present a novel approach to stain normalization in histopathology images. The method is based on nonlinear mapping of a source image to a target image using a representation derived from color deconvolution. Color deconvolution is a method to obtain stain concentration values when the stain matrix, describing how the color is affected by the stain concentration, is given. Rather than relying on standard stain matrices, which may be inappropriate for a given image, we propose the use of a color-based classifier that incorporates a novel stain color descriptor to calculate image-specific stain matrix. In order to demonstrate the efficacy of the proposed stain matrix estimation and stain normalization methods, they are applied to the problem of tumor segmentation in breast histopathology images. The experimental results suggest that the paradigm of color normalization, as a preprocessing step, can significantly help histological image analysis algorithms to demonstrate stable performance which is insensitive to imaging conditions in general and scanner variations in particular.

The proportion of tumour cells is an independent predictor for survival in colorectal cancer patients

Background:The proportion of epithelial and stromal cells in tumours is thought to have an important role in the progression of epithelial malignancy. We aimed to determine whether the relative proportion of tumour (PoT) was related to survival in colorectal cancer.Methods:The PoT at the luminal surface was measured by point counting using virtual tissue sections in a series of 145 colorectal cancer cases. The relationship of PoT to clinicopathological parameters including cancer-specific survival was analysed. Modified receiver operating characteristic curves were used to determine the optimum cut off points to dichotomise the data for survival analyses.Results:Tumours with PoT-low (⩽47%) were associated with significantly lower cancer-specific survival when compared to PoT-high (hazard ratio (HR)=2.087, 95% CI=1.088–4.003, P=0.024). On sub-analysis, the prognostic effect remained significant in colonic tumours (HR=2.474, 95% CI=1.132–5.408, P=0.019) and tumour, node, metastasis stage III disease (HR=3.480, 95% CI=0.325–9.136, P=0.007). Multivariate Cox regression analysis demonstrated that PoT was an independent prognostic marker when adjusted for age, T stage, N stage and extramural vascular invasion (P=0.017).Conclusion:This study suggests that a low proportion of tumour cells in colorectal cancer is related to poor cancer-specific survival. A relatively quick, inexpensive and well-established method such as point counting on diagnostic tissue sections could be used to identify a subset of patients who may benefit from adjuvant therapy.

Toward routine use of 3D histopathology as a research tool.

Three-dimensional (3D) reconstruction and examination of tissue at microscopic resolution have significant potential to enhance the study of both normal and disease processes, particularly those involving structural changes or those in which the spatial relationship of disease features is important. Although other methods exist for studying tissue in 3D, using conventional histopathological features has significant advantages because it allows for conventional histopathological staining and interpretation techniques. Until now, its use has not been routine in research because of the technical difficulty in constructing 3D tissue models. We describe a novel system for 3D histological reconstruction, integrating whole-slide imaging (virtual slides), image serving, registration, and visualization into one user-friendly package. It produces high-resolution 3D reconstructions with minimal user interaction and can be used in a histopathological laboratory without input from computing specialists. It uses a novel method for slice-to-slice image registration using automatic registration algorithms custom designed for both virtual slides and histopathological images. This system has been applied to >300 separate 3D volumes from eight different tissue types, using a total of 5500 virtual slides comprising 1.45 TB of primary image data. Qualitative and quantitative metrics for the accuracy of 3D reconstruction are provided, with measured registration accuracy approaching 120 μm for a 1-cm piece of tissue. Both 3D tissue volumes and generated 3D models are presented for four demonstrator cases.

Sinusoidal Obstructive Syndrome Diagnosed With Superparamagnetic Iron Oxide–Enhanced Magnetic Resonance Imaging in Patients With Chemotherapy-Treated Colorectal Liver Metastases

PURPOSE To assess the predictive value of superparamagnetic iron oxide (SPIO) -enhanced T2-weighted gradient echo (GRE) imaging to determine the presence and severity of sinusoidal obstructive syndrome (SOS). PATIENTS AND METHODS Sixty hepatic resection patients with colorectal metastases treated with chemotherapy underwent unenhanced magnetic resonance imaging (MRI) followed by T2-weighted GRE sequences obtained after SPIO. The images were reviewed in consensus by two experienced observers who determined the presence and severity of linear and reticular hyperintensities, indicating SOS-type liver injury, using a 4-point ordinal scale. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) with 95% CIs for the detection of SOS were calculated. RESULTS Twenty-four of 60 patients had moderate to severe SOS on MRI. MRI achieved a sensitivity of 87% (95% CI, 66% to 97%), specificity of 89% (95% CI, 75% to 97%), PPV of 83% (95% CI, 63% to 95%), and NPV of 92% (95% CI, 77% to 98%). SOS was never found at surgery or histology in patients whose background liver parenchyma was normal on SPIO-enhanced MRI. CONCLUSION SOS is present in a significant proportion of patients with treated colorectal metastases and is effectively detected on SPIO-enhanced T2-weighted GRE images.

Guidelines and considerations for conducting experiments using tissue microarrays

Tissue microarrays (TMAs) represent a powerful method for undertaking large‐scale tissue‐based biomarker studies. While TMAs offer several advantages, there are a number of issues specific to their use which need to be considered when employing this method. Given the investment in TMA‐based research, guidance on design and execution of experiments will be of benefit and should help researchers new to TMA‐based studies to avoid known pitfalls. Furthermore, a consensus on quality standards for TMA‐based experiments should improve the robustness and reproducibility of studies, thereby increasing the likelihood of identifying clinically useful biomarkers. In order to address these issues, the National Cancer Research Institute Biomarker and Imaging Clinical Studies Group organized a 1‐day TMA workshop held in Nottingham in May 2012. The document herein summarizes the conclusions from the workshop. It includes guidance and considerations on all aspects of TMA‐based research, including the pre‐analytical stages of experimental design, the analytical stages of data acquisition, and the postanalytical stages of data analysis. A checklist is presented which can be used both for planning a TMA experiment and interpreting the results of such an experiment. For studies of cancer biomarkers, this checklist could be used as a supplement to the REMARK guidelines.

Virtual reality Powerwall versus conventional microscope for viewing pathology slides: an experimental comparison.

Aims:  Virtual slides could replace the conventional microscope. However, it can take 60% longer to make a diagnosis with a virtual slide, due to the small display size and inadequate user interface of current systems. The aim was to create and test a virtual reality (VR) microscope using a Powerwall (a high‐resolution array of 28 computer screens) for viewing virtual slides more efficiently.

3D reconstruction of multiple stained histology images.

Context: Three dimensional (3D) tissue reconstructions from the histology images with different stains allows the spatial alignment of structural and functional elements highlighted by different stains for quantitative study of many physiological and pathological phenomena. This has significant potential to improve the understanding of the growth patterns and the spatial arrangement of diseased cells, and enhance the study of biomechanical behavior of the tissue structures towards better treatments (e.g. tissue-engineering applications). Methods: This paper evaluates three strategies for 3D reconstruction from sets of two dimensional (2D) histological sections with different stains, by combining methods of 2D multi-stain registration and 3D volumetric reconstruction from same stain sections. Setting and Design: The different strategies have been evaluated on two liver specimens (80 sections in total) stained with Hematoxylin and Eosin (H and E), Sirius Red, and Cytokeratin (CK) 7. Results and Conclusion: A strategy of using multi-stain registration to align images of a second stain to a volume reconstructed by same-stain registration results in the lowest overall error, although an interlaced image registration approach may be more robust to poor section quality.

Consistency and Standardization of Color in Medical Imaging: a Consensus Report

This article summarizes the consensus reached at the Summit on Color in Medical Imaging held at the Food and Drug Administration (FDA) on May 8–9, 2013, co-sponsored by the FDA and ICC (International Color Consortium). The purpose of the meeting was to gather information on how color is currently handled by medical imaging systems to identify areas where there is a need for improvement, to define objective requirements, and to facilitate consensus development of best practices. Participants were asked to identify areas of concern and unmet needs. This summary documents the topics that were discussed at the meeting and recommendations that were made by the participants. Key areas identified where improvements in color would provide immediate tangible benefits were those of digital microscopy, telemedicine, medical photography (particularly ophthalmic and dental photography), and display calibration. Work in these and other related areas has been started within several professional groups, including the creation of the ICC Medical Imaging Working Group.

The Diagnostic Concordance of Whole Slide Imaging and Light Microscopy: A Systematic Review

CONTEXT -Light microscopy (LM) is considered the reference standard for diagnosis in pathology. Whole slide imaging (WSI) generates digital images of cellular and tissue samples and offers multiple advantages compared with LM. Currently, WSI is not widely used for primary diagnosis. The lack of evidence regarding concordance between diagnoses rendered by WSI and LM is a significant barrier to both regulatory approval and uptake. OBJECTIVE -To examine the published literature on the concordance of pathologic diagnoses rendered by WSI compared with those rendered by LM. DATA SOURCES -We conducted a systematic review of studies assessing the concordance of pathologic diagnoses rendered by WSI and LM. Studies were identified following a systematic search of Medline (Medline Industries, Mundelein, Illinois), Medline in progress (Medline Industries), EMBASE (Elsevier, Amsterdam, the Netherlands), and the Cochrane Library (Wiley, London, England), between 1999 and March 2015. CONCLUSIONS -Thirty-eight studies were included in the review. The mean diagnostic concordance of WSI and LM, weighted by the number of cases per study, was 92.4%. The weighted mean κ coefficient between WSI and LM was 0.75, signifying substantial agreement. Of the 30 studies quoting percentage concordance, 18 (60%) showed a concordance of 90% or greater, of which 10 (33%) showed a concordance of 95% or greater. This review found evidence to support a high level of diagnostic concordance. However, there were few studies, many were small, and they varied in quality, suggesting that further validation studies are still needed.

Virtual reality microscope versus conventional microscope regarding time to diagnosis: an experimental study

Aims:  To create and evaluate a virtual reality (VR) microscope that is as efficient as the conventional microscope, seeking to support the introduction of digital slides into routine practice.