Bas Hulsken

Real-time deformable registration of multi-modal whole slides for digital pathology

Digital pathology provides new ways to visualize tissue slides and enables new workflows for analyzing these slides. Analogous to radiology, adjacent tissue sections prepared with different stains or biomarkers (e.g. H&E, IHC, special stains, or ISH; chromogenic or fluorescent) may be seen as different modalities, each representing different structural and/or functional information. Today, the anatomic pathologist views multiple glass slides using an optical microscope and then combines the information in their head to reach a (diagnostic) opinion. Moreover, due to the nature of the slide preparation and digitization process, the tissue and its features do not have the exact same morphology, appearance, or spatial alignment, making it difficult to find the same region on adjacent slides. To address such concerns, this paper presents a method for the spatial alignment of multi-modal whole slide digital microscopy images. To remain practical, the described method employs a two-step registration strategy designed to reduce computation time: the first step computes a B-spline deformable transform on low-resolution images prior to visualization, the second step applies the precomputed transformation only to the high-resolution region currently being viewed. The proposed method is demonstrated using a number of cases comprising H&E and IHC stained slides. These results indicate the feasibility of deformable registration for spatial alignment of multi-modal whole slide digital microscopy images within practical time constraints.

Color accuracy and reproducibility in whole slide imaging scanners.

Abstract We propose a workflow for color reproduction in whole slide imaging (WSI) scanners, such that the colors in the scanned images match to the actual slide color and the inter-scanner variation is minimum. We describe a new method of preparation and verification of the color phantom slide, consisting of a standard IT8-target transmissive film, which is used in color calibrating and profiling the WSI scanner. We explore several International Color Consortium (ICC) compliant techniques in color calibration/profiling and rendering intents for translating the scanner specific colors to the standard display (sRGB) color space. Based on the quality of the color reproduction in histopathology slides, we propose the matrix-based calibration/profiling and absolute colorimetric rendering approach. The main advantage of the proposed workflow is that it is compliant to the ICC standard, applicable to color management systems in different platforms, and involves no external color measurement devices. We quantify color difference using the CIE-DeltaE2000 metric, where DeltaE values below 1 are considered imperceptible. Our evaluation on 14 phantom slides, manufactured according to the proposed method, shows an average inter-slide color difference below 1 DeltaE. The proposed workflow is implemented and evaluated in 35 WSI scanners developed at Philips, called the Ultra Fast Scanners (UFS). The color accuracy, measured as DeltaE between the scanner reproduced colors and the reference colorimetric values of the phantom patches, is improved on average to 3.5 DeltaE in calibrated scanners from 10 DeltaE in uncalibrated scanners. The average inter-scanner color difference is found to be 1.2 DeltaE. The improvement in color performance upon using the proposed method is apparent with the visual color quality of the tissue scans.

Optical quality assessment of whole slide imaging systems for digital pathology

Whole Slide Imaging (WSI) systems are high-throughput automated microscopes for digital pathology applications. We present a method for testing and monitoring the optical quality of WSI-systems using a measurement of the through-focus Optical Transfer Function (OTF) obtained from the edge response of a custom made resolution target, composed of sagittal and tangential edges. This enables quantitative analysis of a number of primary aberrations. The curvature of the best focus as a function of spatial frequency is indicative for spherical aberration, the argument of the OTF quantifies for coma, and the best focus as a function of field position for sagittal and tangential edges allows assessment of astigmatism and field curvature. The statistical error in the determined aberrations is typically below 20 mλ. We use the method to compare different tube lens designs and to study the effect of objective lens aging. The results are in good agreement with direct measurement of aberrations based on Shack-Hartmann wavefront sensing with a typical error ranging from 10 mλ to 40 mλ.

Shack-Hartmann sensor based optical quality testing of whole slide imaging systems for digital pathology

Whole Slide Imaging (WSI) systems are used in the emerging field of digital pathology for capturing high-resolution images of tissue slides at high throughput. We present a technique to measure the optical aberrations of WSI systems using a Shack-Hartmann wavefront sensor as a function of field position. The resulting full-field aberration maps for the lowest order astigmatism and coma are analyzed using nodal aberration theory. According to this theory two coefficients describe the astigmatism and coma inherent to the optical design and another six coefficients are needed to describe the cumulative effects of all possible misalignments on astigmatism and coma. The nodal aberration theory appears to fit well to the experimental data. We have measured and analyzed the full-field aberration maps for two different objective lens-tube lens assemblies and found that only the optical design related astigmatism coefficient differed substantially between the two cases, but in agreement with expectations. We have also studied full-field aberration maps for intentional decenter and tilt and found that these affect the misalignment coefficient for constant coma (decenter) and the misalignment coefficient for linear astigmatism (tilt), while keeping all other nodal aberration theory coefficients constant.

Color accuracy and reproducibility in whole slide imaging scanners

In this paper, we propose a work-flow for color reproduction in whole slide imaging (WSI) scanners such that the colors in the scanned images match to the actual slide color and the inter scanner variation is minimum. We describe a novel method of preparation and verification of the color phantom slide, consisting of a standard IT8- target transmissive film, which is used in color calibrating and profiling the WSI scanner. We explore several ICC compliant techniques in color calibration/profiling and rendering intents for translating the scanner specific colors to the standard display (sRGB) color-space. Based on the quality of color reproduction in histopathology tissue slides, we propose the matrix-based calibration/profiling and absolute colorimetric rendering approach. The main advantage of the proposed work-ow is that it is compliant to the ICC standard, applicable to color management systems in different platforms, and involves no external color measurement devices. We measure objective color performance using CIE-DeltaE2000 metric, where DeltaE values below 1 is considered imperceptible. Our evaluation 14 phantom slides, manufactured according to the proposed method, show an average inter-slide color difference below 1 DeltaE. The proposed work-flow is implemented and evaluated in 35 Philips Ultra Fast Scanners (UFS). The results show that the average color difference between a scanner and the reference is 3.5 DeltaE, and among the scanners is 3.1 DeltaE. The improvement on color performance upon using the proposed method is apparent on the visual color quality of the tissues scans.

A quantitative approach to evaluate image quality of whole slide imaging scanners

Context: The quality of images produced by whole slide imaging (WSI) scanners has a direct influence on the readers′ performance and reliability of the clinical diagnosis. Therefore, WSI scanners should produce not only high quality but also consistent quality images. Aim: We aim to evaluate reproducibility of WSI scanners based on the quality of images produced over time and among multiple scanners. The evaluation is independent of content or context of test specimen. Methods: The ultimate judge of image quality is a pathologist, however, subjective evaluations are heavily influenced by the complexity of a case and subtle variations introduced by a scanner can be easily overlooked. Therefore, we employed a quantitative image quality assessment method based on clinically relevant parameters, such as sharpness and brightness, acquired in a survey of pathologists. The acceptable level of quality per parameter was determined in a subjective study. The evaluation of scanner reproducibility was conducted with Philips Ultra-Fast Scanners. A set of 36 HercepTest™ slides were used in three sub-studies addressing variations due to systems and time, producing 8640 test images for evaluation. Results: The results showed that the majority of images in all the sub-studies are within the acceptable quality level; however, some scanners produce higher quality images more often than others. The results are independent of case types, and they match our perception of quality. Conclusion: The quantitative image quality assessment method was successfully applied in the HercepTest™ slides to evaluate WSI scanner reproducibility. The proposed method is generic and applicable to any other types of slide stains and scanners.

Trough-Focus OTF Based Optical Quality Testing of Whole Slide Scanners for Digital Pathology

We measure the through-focus OTF of whole slide scanners for optical quality testing and monitoring. Analysis of the OTF data gives a system level evaluation of astigmatism, field curvature, chromatic aberrations, coma and spherical aberration.