Detecting prostatic adenocarcinoma from digitized histology using a multi-scale hierarchical classification approach

Attention Layer-Based Multidimensional Feature Extraction for Diagnosis of Lung Cancer

At present, early lung cancer screening is mainly based on radiologists' experience in diagnosing benign and malignant pulmonary nodules by lung CT images. On the other hand, intraoperative rapid freezing pathology needs to analyse the invasive adenocarcinoma nodules with the worst recovery in adenocarcinoma. Moreover, rapid freezing pathology has a low diagnostic accuracy for small-diameter nodules. Because of the above problems, an algorithm for diagnosing invasive adenocarcinoma nodules in ground-glass pulmonary nodules is based on CT images. According to the nodule space information and plane features, sample data of different dimensions are designed, namely, 3D space and 2D plane feature samples. The network structure is designed based on the attention mechanism and residual learning unit; 2D and 3D neural networks are along built. By fusing the feature vectors extracted from networks of different dimensions, the diagnosis results of invasive adenocarcinoma nodules are finally obtained. The algorithm was studied on 1760 ground-glass nodules with 5-20 mm diameter collected from a city chest hospital with surgical and pathological results. There were 340 nodules with invasive adenocarcinoma and 340 with noninvasive adenocarcinoma. A total of 1420 invasive nodule samples were cross-validated on this example dataset. The classification accuracy of the algorithm was 82.7%, the sensitivity was 82.9%, and the specificity was 82.6%.

HistoQC: An Open-Source Quality Control Tool for Digital Pathology Slides

PURPOSE

Digital pathology (DP), referring to the digitization of tissue slides, is beginning to change the landscape of clinical diagnostic workflows and has engendered active research within the area of computational pathology. One of the challenges in DP is the presence of artefacts and batch effects, unintentionally introduced during both routine slide preparation (eg, staining, tissue folding) and digitization (eg, blurriness, variations in contrast and hue). Manual review of glass and digital slides is laborious, qualitative, and subject to intra- and inter-reader variability. Therefore, there is a critical need for a reproducible automated approach of precisely localizing artefacts to identify slides that need to be reproduced or regions that should be avoided during computational analysis.

METHODS

Here we present HistoQC, a tool for rapidly performing quality control to not only identify and delineate artefacts but also discover cohort-level outliers (eg, slides stained darker or lighter than others in the cohort). This open-source tool employs a combination of image metrics (eg, color histograms, brightness, contrast), features (eg, edge detectors), and supervised classifiers (eg, pen detection) to identify artefact-free regions on digitized slides. These regions and metrics are presented to the user via an interactive graphical user interface, facilitating artefact detection through real-time visualization and filtering. These same metrics afford users the opportunity to explicitly define acceptable tolerances for their workflows.

RESULTS

The output of HistoQC on 450 slides from The Cancer Genome Atlas was reviewed by two pathologists and found to be suitable for computational analysis more than 95% of the time.

CONCLUSION

These results suggest that HistoQC could provide an automated, quantifiable, quality control process for identifying artefacts and measuring slide quality, in turn helping to improve both the repeatability and robustness of DP workflows.

Estimation of Fine-Scale Histologic Features at Low Magnification

CONTEXT.—

Whole-slide imaging has ushered in a new era of technology that has fostered the use of computational image analysis for diagnostic support and has begun to transfer the act of analyzing a slide to computer monitors. Due to the overwhelming amount of detail available in whole-slide images, analytic procedures-whether computational or visual-often operate at magnifications lower than the magnification at which the image was acquired. As a result, a corresponding reduction in image resolution occurs. It is unclear how much information is lost when magnification is reduced, and whether the rich color attributes of histologic slides can aid in reconstructing some of that information.

OBJECTIVE.—

To examine the correspondence between the color and spatial properties of whole-slide images to elucidate the impact of resolution reduction on the histologic attributes of the slide.

DESIGN.—

We simulated image resolution reduction and modeled its effect on classification of the underlying histologic structure. By harnessing measured histologic features and the intrinsic spatial relationships between histologic structures, we developed a predictive model to estimate the histologic composition of tissue in a manner that exceeds the resolution of the image.

RESULTS.—

Reduction in resolution resulted in a significant loss of the ability to accurately characterize histologic components at magnifications less than ×10. By utilizing pixel color, this ability was improved at all magnifications.

CONCLUSIONS.—

Multiscale analysis of histologic images requires an adequate understanding of the limitations imposed by image resolution. Our findings suggest that some of these limitations may be overcome with computational modeling.

Fractal analysis and the diagnostic usefulness of silver staining nucleolar organizer regions in prostate adenocarcinoma

Pathological diagnosis of prostate adenocarcinoma often requires complementary methods. On prostate biopsy tissue from 39 patients including benign nodular hyperplasia (BNH), atypical adenomatous hyperplasia (AAH), and adenocarcinomas, we have performed combined histochemical-immunohistochemical stainings for argyrophilic nucleolar organizer regions (AgNORs) and glandular basal cells. After ascertaining the pathology, we have analyzed the number, roundness, area, and fractal dimension of individual AgNORs or of their skeleton-filtered maps. We have optimized here for the first time a combination of AgNOR morphological denominators that would reflect best the differences between these pathologies. The analysis of AgNORs' roundness, averaged from large composite images, revealed clear-cut lower values in adenocarcinomas compared to benign and atypical lesions but with no differences between different Gleason scores. Fractal dimension (FD) of AgNOR silhouettes not only revealed significant lower values for global cancer images compared to AAH and BNH images, but was also able to differentiate between Gleason pattern 2 and Gleason patterns 3–5 adenocarcinomas. Plotting the frequency distribution of the FDs for different pathologies showed clear differences between all Gleason patterns and BNH. Together with existing morphological classifiers, AgNOR analysis might contribute to a faster and more reliable machine-assisted screening of prostatic adenocarcinoma, as an essential aid for pathologists.

Automated image based prominent nucleoli detection

Introduction:

Nucleolar changes in cancer cells are one of the cytologic features important to the tumor pathologist in cancer assessments of tissue biopsies. However, inter-observer variability and the manual approach to this work hamper the accuracy of the assessment by pathologists. In this paper, we propose a computational method for prominent nucleoli pattern detection.

Materials and Methods:

Thirty-five hematoxylin and eosin stained images were acquired from prostate cancer, breast cancer, renal clear cell cancer and renal papillary cell cancer tissues. Prostate cancer images were used for the development of a computer-based automated prominent nucleoli pattern detector built on a cascade farm. An ensemble of approximately 1000 cascades was constructed by permuting different combinations of classifiers such as support vector machines, eXclusive component analysis, boosting, and logistic regression. The output of cascades was then combined using the RankBoost algorithm. The output of our prominent nucleoli pattern detector is a ranked set of detected image patches of patterns of prominent nucleoli.

Results:

The mean number of detected prominent nucleoli patterns in the top 100 ranked detected objects was 58 in the prostate cancer dataset, 68 in the breast cancer dataset, 86 in the renal clear cell cancer dataset, and 76 in the renal papillary cell cancer dataset. The proposed cascade farm performs twice as good as the use of a single cascade proposed in the seminal paper by Viola and Jones. For comparison, a naive algorithm that randomly chooses a pixel as a nucleoli pattern would detect five correct patterns in the first 100 ranked objects.

Conclusions:

Detection of sparse nucleoli patterns in a large background of highly variable tissue patterns is a difficult challenge our method has overcome. This study developed an accurate prominent nucleoli pattern detector with the potential to be used in the clinical settings.

A novel HMM distributed classifier for the detection of gait phases by means of a wearable inertial sensor network

In this work, we decided to apply a hierarchical weighted decision, proposed and used in other research fields, for the recognition of gait phases. The developed and validated novel distributed classifier is based on hierarchical weighted decision from outputs of scalar Hidden Markov Models (HMM) applied to angular velocities of foot, shank, and thigh. The angular velocities of ten healthy subjects were acquired via three uni-axial gyroscopes embedded in inertial measurement units (IMUs) during one walking task, repeated three times, on a treadmill. After validating the novel distributed classifier and scalar and vectorial classifiers-already proposed in the literature, with a cross-validation, classifiers were compared for sensitivity, specificity, and computational load for all combinations of the three targeted anatomical segments. Moreover, the performance of the novel distributed classifier in the estimation of gait variability in terms of mean time and coefficient of variation was evaluated. The highest values of specificity and sensitivity (>0.98) for the three classifiers examined here were obtained when the angular velocity of the foot was processed. Distributed and vectorial classifiers reached acceptable values (>0.95) when the angular velocity of shank and thigh were analyzed. Distributed and scalar classifiers showed values of computational load about 100 times lower than the one obtained with the vectorial classifier. In addition, distributed classifiers showed an excellent reliability for the evaluation of mean time and a good/excellent reliability for the coefficient of variation. In conclusion, due to the better performance and the small value of computational load, the here proposed novel distributed classifier can be implemented in the real-time application of gait phases recognition, such as to evaluate gait variability in patients or to control active orthoses for the recovery of mobility of lower limb joints.

How bioinformatics influences health informatics: usage of biomolecular sequences, expression profiles and automated microscopic image analyses for clinical needs and public health

ABSTRACT

The currently hyped expectation of personalized medicine is often associated with just achieving the information technology led integration of biomolecular sequencing, expression and histopathological bioimaging data with clinical records at the individual patients' level as if the significant biomedical conclusions would be its more or less mandatory result. It remains a sad fact that many, if not most biomolecular mechanisms that translate the human genomic information into phenotypes are not known and, thus, most of the molecular and cellular data cannot be interpreted in terms of biomedically relevant conclusions. Whereas the historical trend will certainly be into the general direction of personalized diagnostics and cures, the temperate view suggests that biomedical applications that rely either on the comparison of biomolecular sequences and/or on the already known biomolecular mechanisms have much greater chances to enter clinical practice soon. In addition to considering the general trends, we exemplarily review advances in the area of cancer biomarker discovery, in the clinically relevant characterization of patient-specific viral and bacterial pathogens (with emphasis on drug selection for influenza and enterohemorrhagic E. coli) as well as progress in the automated assessment of histopathological images. As molecular and cellular data analysis will become instrumental for achieving desirable clinical outcomes, the role of bioinformatics and computational biology approaches will dramatically grow.

AUTHOR SUMMARY

With DNA sequencing and computers becoming increasingly cheap and accessible to the layman, the idea of integrating biomolecular and clinical patient data seems to become a realistic, short-term option that will lead to patient-specific diagnostics and treatment design for many diseases such as cancer, metabolic disorders, inherited conditions, etc. These hyped expectations will fail since many, if not most biomolecular mechanisms that translate the human genomic information into phenotypes are not known yet and, thus, most of the molecular and cellular data collected will not lead to biomedically relevant conclusions. At the same time, less spectacular biomedical applications based on biomolecular sequence comparison and/or known biomolecular mechanisms have the potential to unfold enormous potential for healthcare and public health. Since the analysis of heterogeneous biomolecular data in context with clinical data will be increasingly critical, the role of bioinformatics and computational biology will grow correspondingly in this process.

Perceptual analysis of the reading of dermatopathology virtual slides by pathology residents

CONTEXT

The process by which pathologists arrive at a given diagnosis-a combination of their slide exploration strategy, perceptual information gathering, and cognitive decision making-has not been thoroughly explored, and many questions remain unanswered.

OBJECTIVE

To determine how pathology residents learn to diagnose inflammatory skin dermatoses, we contrasted the slide exploration strategy, perceptual capture of relevant histopathologic findings, and cognitive integration of identified features between 2 groups of residents, those who had and those who had not undergone their dermatopathology rotation.

DESIGN

Residents read a case set of 20 virtual slides (10 depicting nodular and diffuse dermatitis and 10 depicting subepidermal vesicular dermatitis), using an in-house-developed interface. We recorded residents' reports of diagnostic findings, conjectured diagnostic hypotheses, and final (or differential) diagnosis for each case, and time stamped each interaction with the interface. We created search maps of residents' slide exploration strategy.

RESULTS

No statistically significant differences were observed between the resident groups in the number of correctly or incorrectly reported diagnostic findings, but residents with dermatopathology training generated significantly more correct hypotheses (mean improvement of 88.5%) and correct diagnoses (70% of all correct diagnoses).

CONCLUSIONS

Two types of slide exploration strategy were identified for both groups: (1) a focused and efficient search, observed when the final diagnosis was correct; and (2) a more dispersed, time-consuming strategy, observed when the final diagnosis was incorrect. This difference was statistically significant, and it suggests that initial interpretation of a slide may bias further slide exploration.

Multi-field-of-view strategy for image-based outcome prediction of multi-parametric estrogen receptor-positive breast cancer histopathology: Comparison to Oncotype DX

In this paper, we attempt to quantify the prognostic information embedded in multi-parametric histologic biopsy images to predict disease aggressiveness in estrogen receptor-positive (ER+) breast cancers (BCa). The novel methodological contribution is in the use of a multi-field-of-view (multi-FOV) framework for integrating image-based information from differently stained histopathology slides. The multi-FOV approach involves a fixed image resolution while simultaneously integrating image descriptors from many FOVs corresponding to different sizes. For each study, the corresponding risk score (high scores reflecting aggressive disease and vice versa), predicted by a molecular assay (Oncotype DX), is available and serves as the surrogate ground truth for long-term patient outcome. Using the risk scores, a trained classifier is used to identify disease aggressiveness for each FOV size. The predictions for each FOV are then combined to yield the final prediction of disease aggressiveness (good, intermediate, or poor outcome). Independent multi-FOV classifiers are constructed for (1) 50 image features describing the spatial arrangement of cancer nuclei (via Voronoi diagram, Delaunay triangulation, and minimum spanning tree graphs) in H and E stained histopathology and (2) one image feature describing the vascular density in CD34 IHC stained histopathology. In a cohort of 29 patients, the multi-FOV classifiers obtained by combining information from the H and E and CD34 IHC stained channels were able to distinguish low- and high-risk patients with an accuracy of 0.91 ± 0.02 and a positive predictive value of 0.94 ± 0.10, suggesting that a purely image-based assay could potentially replace more expensive molecular assays for making disease prognostic predictions.

Computer-aided identification of prostatic adenocarcinoma: Segmentation of glandular structures

Background:

Identification of individual prostatic glandular structures is an important prerequisite to quantitative histological analysis of prostate cancer with the aid of a computer. We have developed a computer method to segment individual glandular units and to extract quantitative image features, for computer identification of prostatic adenocarcinoma.

Methods:

Two sets of digital histology images were used: database I (n = 57) for developing and testing the computer technique, and database II (n = 116) for independent validation. The segmentation technique was based on a k-means clustering and a region-growing method. Computer segmentation results were evaluated subjectively and also compared quantitatively against manual gland outlines, using the Jaccard similarity measure. Quantitative features that were extracted from the computer segmentation results include average gland size, spatial gland density, and average gland circularity. Linear discriminant analysis (LDA) was used to combine quantitative image features. Classification performance was evaluated with receiver operating characteristic (ROC) analysis and the area under the ROC curve (AUC).

Results:

Jaccard similarity coefficients between computer segmentation and manual outlines of individual glands were between 0.63 and 0.72 for non-cancer and between 0.48 and 0.54 for malignant glands, respectively, similar to an interobserver agreement of 0.79 for non-cancer and 0.75 for malignant glands, respectively. The AUC value for the features of average gland size and gland density combined via LDA was 0.91 for database I and 0.96 for database II.

Conclusions:

Using a computer, we are able to delineate individual prostatic glands automatically and identify prostatic adenocarcinoma accurately, based on the quantitative image features extracted from computer-segmented glandular structures.

SHIRAZ: an automated histology image annotation system for zebrafish phenomics

Histological characterization is used in clinical and research contexts as a highly sensitive method for detecting the morphological features of disease and abnormal gene function. Histology has recently been accepted as a phenotyping method for the forthcoming Zebrafish Phenome Project, a large-scale community effort to characterize the morphological, physiological, and behavioral phenotypes resulting from the mutations in all known genes in the zebrafish genome. In support of this project, we present a novel content-based image retrieval system for the automated annotation of images containing histological abnormalities in the developing eye of the larval zebrafish.

Histopathological image analysis: a review

Over the past decade, dramatic increases in computational power and improvement in image analysis algorithms have allowed the development of powerful computer-assisted analytical approaches to radiological data. With the recent advent of whole slide digital scanners, tissue histopathology slides can now be digitized and stored in digital image form. Consequently, digitized tissue histopathology has now become amenable to the application of computerized image analysis and machine learning techniques. Analogous to the role of computer-assisted diagnosis (CAD) algorithms in medical imaging to complement the opinion of a radiologist, CAD algorithms have begun to be developed for disease detection, diagnosis, and prognosis prediction to complement the opinion of the pathologist. In this paper, we review the recent state of the art CAD technology for digitized histopathology. This paper also briefly describes the development and application of novel image analysis technology for a few specific histopathology related problems being pursued in the United States and Europe.

Histopathological image analysis: a review

Over the past decade, dramatic increases in computational power and improvement in image analysis algorithms have allowed the development of powerful computer-assisted analytical approaches to radiological data. With the recent advent of whole slide digital scanners, tissue histopathology slides can now be digitized and stored in digital image form. Consequently, digitized tissue histopathology has now become amenable to the application of computerized image analysis and machine learning techniques. Analogous to the role of computer-assisted diagnosis (CAD) algorithms in medical imaging to complement the opinion of a radiologist, CAD algorithms have begun to be developed for disease detection, diagnosis, and prognosis prediction to complement the opinion of the pathologist. In this paper, we review the recent state of the art CAD technology for digitized histopathology. This paper also briefly describes the development and application of novel image analysis technology for a few specific histopathology related problems being pursued in the United States and Europe.

Digital pathology: a tool for 21st century neuropathology

Digital pathology represents an electronic environment for performing pathologic analysis and managing the information associated with this activity. The technology to create and support digital pathology has largely developed over the last decade. The use of digital pathology tools is essential to adapt and lead in the rapidly changing environment of 21st century neuropathology. The utility of digital pathology has already been demonstrated by pathologists in several areas including consensus reviews, quality assurance (Q/A), tissue microarrays (TMAs), education and proficiency testing. These utilities notwithstanding, interface issues, storage and image formatting all present challenges to the integration of digital pathology into the neuropathology work environment. With continued technologic improvements, as well as the introduction of fluorescent side scanning and multispectral detection, future developments in digital pathology offer the promise of adding powerful analytic tools to the pathology work environment. The integration of digital pathology with biorepositories offers particular promise for neuropathologists engaged in tissue banking. The utilization of these tools will be essential for neuropathologists to continue as leaders in diagnostics, translational research and basic science in the 21st century.