Digital pathology in clinical use: where are we now and what is holding us back?

Whole slide imaging is being used increasingly in research applications and in frozen section, consultation and external quality assurance practice. Digital pathology, when integrated with other digital tools such as barcoding, specimen tracking and digital dictation, can be integrated into the histopathology workflow, from specimen accession to report sign-out. These elements can bring about improvements in the safety, quality and efficiency of a histopathology department. The present paper reviews the evidence for these benefits. We then discuss the challenges of implementing a fully digital pathology workflow, including the regulatory environment, validation of whole slide imaging and the evidence for the design of a digital pathology workstation

Experiments with a novel CCD stellar polarimeter

Experiments and observations have been undertaken with "bread-board" equipment to explore the potential of a "ring" stellar polarimeter with a CCD camera, rather than photographic plates used in Treanor's (1968) original instrument. By spreading the polarimetric signal over a large number of pixels on the detector, design prediction suggests that the polarimetric accuracy could be ~Δρ±0.00001 or ±0.001% per frame or even better. Although the photon accumulations suggest that this was achieved, instabilities in the employed crude modulator system provided frame to frame measurements with a greater than expected scatter. Software was developed to reduce the data in a simple way. With a design using more professional components and perhaps with more sophisticated reduction procedures, the full potential of the method should be achievable with the prospect of high precision polarimetry of the brighter stars. As an experimental bonus, the employed CCD chip was found to be free from any measurable polarizational sensitivity

Stain guided mean-shift filtering in automatic detection of human tissue nuclei

Background: As a critical technique in a digital pathology laboratory, automatic nuclear detection has been investigated for more than one decade. Conventional methods work on the raw images directly whose color/intensity homogeneity within tissue/cell areas are undermined due to artefacts such as uneven staining, making the subsequent binarization process prone to error. This paper concerns detecting cell nuclei automatically from digital pathology images by enhancing the color homogeneity as a pre-processing step. Methods: Unlike previous watershed based algorithms relying on post-processing of the watershed, we present a new method that incorporates the staining information of pathological slides in the analysis. This pre-processing step strengthens the color homogeneity within the nuclear areas as well as the background areas, while keeping the nuclear edges sharp. Proof of convergence for the proposed algorithm is also provided. After pre-processing, Otsu's threshold is applied to binarize the image, which is further segmented via watershed. To keep a proper compromise between removing overlapping and avoiding over-segmentation, a naive Bayes classifier is designed to refine the splits suggested by the watershed segmentation. Results: The method is validated with 10 sets of 1000 × 1000 pathology images of lymphoma from one digital slide. The mean precision and recall rates are 87% and 91%, corresponding to a mean F-score equal to 89%. Standard deviations for these performance indicators are 5.1%, 1.6% and 3.2% respectively. Conclusion: The precision/recall performance obtained indicates that the proposed method outperforms several other alternatives. In particular, for nuclear detection, stain guided mean-shift (SGMS) is more effective than the direct application of mean-shift in pre-processing. Our experiments also show that pre-processing the digital pathology images with SGMS gives better results than conventional watershed algorithms. Nevertheless, as only one type of tissue is tested in this paper, a further study is planned to enhance the robustness of the algorithm so that other types of tissues/stains can also be processed reliably

A Novel Approach for the Colour Deconvolution of Multiple Histological Stains

Colour Deconvolution (CD) is a commonly used tool in histological medical image analysis that separates histochemical or immunohistochemical stains into their component parts. Traditional CD uses matrix inversion to change the Red, Green and Blue (RGB) channels of an image into a new domain that is representative of reference colours but this limits the total number of stains that can be separated. This is problematic for histological staining protocols that use more than three stains, such as FAST staining. This limitation has restricted the use of multicolour staining in light microscopy. To address this issue, this paper evaluates the use of Non Negative Matrix Factorisation (NNMF) and Non Negative Least Squares (NNLS) to enable the decomposition of multistained histological sections into its source components. It will be shown that NNLS is better suited to imaging modalities such as Whole Slide Image (WSI) scanners and that the multiple staining metrics produced from a single sample are analogous to those generated by applying single reagents to contiguous tissue sections

Leveraging wall-sized high-resolution displays for comparative genomics analyses of copy number variation

The scale of comparative genomics data frequently overwhelms current data visualization methods on conventional (desktop) displays. This paper describes two types of solution that take advantage of wall-sized high-resolution displays (WHirDs), which have orders of magnitude more display real estate (i.e., pixels) than desktop displays. The first allows users to view detailed graphics of copy number variation (CNV) that were output by existing software. A WHirD's resolution allowed a 10× increase in the granularity of bioinformatics output that was feasible for users to visually analyze, and this revealed a pattern that had previously been smoothed out from the underlying data. The second involved interactive visualization software that was innovative because it uses a music score metaphor to lay out CNV data, overcomes a perceptual distortion caused by amplification/deletion thresholds, uses filtering to reduce graphical data overload, and is the first comparative genomics visualization software that is designed to leverage a WHirD's real estate. In a field evaluation, a clinical user discovered a fundamental error in the way their data had been processed, and established confidence in the software by using it to 'find' known genetic patterns in hepatitis C-driven hepatocellular cancer

A 3D Primary Vessel Reconstruction Framework with Serial Microscopy Images

Three dimensional microscopy images present significant potential to enhance biomedical studies. This paper presents an automated method for quantitative analysis of 3D primary vessel structures with histology whole slide images. With registered microscopy images, we identify primary vessels with an improved variational level set framework at each 2D slide. We propose a Vessel Directed Fitting Energy (VDFE) to provide prior information on vessel wall probability in an energy minimization paradigm. We find the optimal vessel cross-section associations along the image sequence with a two-stage procedure. Vessel mappings are first found between each pair of adjacent slides with a similarity function for four association cases. These bi-slide vessel components are further linked by Bayesian Maximum A Posteriori (MAP) estimation where the posterior probability is modeled as a Markov chain. The efficacy of the proposed method is demonstrated with 54 whole slide microscopy images of sequential sections from a human liver

Liver whole slide image analysis for 3D vessel reconstruction

The emergence of digital pathology has enabled numerous quantitative analyses of histopathology structures. However, most pathology image analyses are limited to two-dimensional datasets, resulting in substantial information loss and incomplete interpretation. To address this, we have developed a complete framework for three-dimensional whole slide image analysis and demonstrated its efficacy on 3D vessel structure analysis with liver tissue sections. The proposed workflow includes components on image registration, vessel segmentation, vessel cross-section association, object interpolation, and volumetric rendering. For 3D vessel reconstruction, a cost function is formulated based on shape descriptors, spatial similarity and trajectory smoothness by taking into account four vessel association scenarios. An efficient entropy-based Relaxed Integer Programming (eRIP) method is proposed to identify the optimal inter-frame vessel associations. The reconstructed 3D vessels are both quantitatively and qualitatively validated. Evaluation results demonstrate high efficiency and accuracy of the proposed method, suggesting its promise to support further 3D vessel analysis with whole slide images

Dynamic platform to recreate an osteoarthritic 3D in vitro model

Osteoarthritis (OA), a prevalent chronic condition with a striking impact on life quality, represents an enormous societal burden that increases greatly as populations’ age. Yet no approved pharmacological intervention, biologic therapy or procedure prevents the progressive destruction of the OA joint. Based on bilayered structures that have been previously suggested for osteochondral (OC) applications (Oliveira et al 2006) and on the potential of methacrylated gelatin (GelMA) and methacrylated gellan gum (MAGG) for different tissue engineering applications (Silva-Correia et al 2013, Tasoglu et al 2014), we set a dynamic platform for the in vitro recreation of an OA 3D in vitro model. Since OA is an inflammatory and degenerative disorder affecting cartilage and subchondral bone, we created 6 hybrid formulations recreating a 3D controlled subchondral bone and cartilage integrated microenvironment. Fat pad adipose derived stem cells (ASCs) were isolated from Hoffa’s body obtained from healthy Patients, characterized by flow cytometry and their performance in the developed 3D structures assessed. GelMA formulation showed the best cell adhesion and proliferation, but the life-time of this one in culture is shorter due to the faster degradation in vitro comparing to MAGG based structures. According to this we proceeded with the best hybrid formulation, GelMA-MAGG 2:1, for OC co-differentiation using a dual-chamber bioreactor designed for the establishment of co-cultures in a single 3D structure (Canadas et al 2014). This approach solved challenges of 3D cell culture in interfaced tissues as OC and will ultimately be used for OA in vitro modelinginfo:eu-repo/semantics/publishedVersio

The night-sky at the Calar Alto Observatory

We present a characterization of the main properties of the night-sky at the Calar Alto observatory for the time period between 2004 and 2007. We use optical spectrophotometric data, photometric calibrated images taken in moonless observing periods, together with the observing conditions regularly monitored at the observatory, such as atmospheric extinction and seeing. We derive, for the first time, the typical moonless night-sky optical spectrum for the observatory. The spectrum shows a strong contamination by different pollution lines, in particular from Mercury lines, which contribution to the sky-brightness in the different bands is of the order of ~0.09 mag, ~0.16 mag and ~0.10 mag in B, V and R respectively. The zenith-corrected values of the moonless night-sky surface brightness are 22.39, 22.86, 22.01, 21.36 and 19.25 mag arcsec^-2 in U, B, V, R and I, which indicates that Calar Alto is a particularly dark site for optical observations up to the I-band. The fraction of astronomical useful nights at the observatory is ~70%, with a ~30% of photometric nights. The typical extinction at the observatory is k_V~0.15 mag in the Winter season, with little dispersion. In summer the extinction has a wider range of values, although it does not reach the extreme peaks observed at other sites. The median seeing for the last two years (2005-6) was ~0.90", being smaller in the Summer (~0.87") than in the Winter (~0.96"). We conclude in general that after 26 years of operations Calar Alto is still a good astronomical site, being a natural candidate for future large aperture optical telescopes.Comment: 16 pages, 5 figures, accepted for publishing in the Publications of Astronomical Society of the Pacific (PASP

A framework for 3D vessel analysis using whole slide images of liver tissue sections

Three-dimensional (3D) high resolution microscopic images have high potential for improving the understanding of both normal and disease processes where structural changes or spatial relationship of disease features are significant. In this paper, we develop a complete framework applicable to 3D pathology analytical imaging, with an application to whole slide images of sequential liver slices for 3D vessel structure analysis. The analysis workflow consists of image registration, segmentation, vessel cross-section association, interpolation, and volumetric rendering. To identify biologically-meaningful correspondence across adjacent slides, we formulate a similarity function for four association cases. The optimal solution is then obtained by constrained Integer Programming. We quantitatively and qualitatively compare our vessel reconstruction results with human annotations. Validation results indicate a satisfactory concordance as measured both by region-based and distance-based metrics. These results demonstrate a promising 3D vessel analysis framework for whole slide images of liver tissue sections