Content-based image retrieval of digitized histopathology in boosted spectrally embedded spaces

Analysis and Validation of Image Search Engines in Histopathology

Searching for similar images in archives of histology and histopathology images is a crucial task that may aid in patient tissue comparison for various purposes, ranging from triaging and diagnosis to prognosis and prediction. Whole slide images (WSIs) are highly detailed digital representations of tissue specimens mounted on glass slides. Matching WSI to WSI can serve as the critical method for patient tissue comparison. In this paper, we report extensive analysis and validation of four search methods bag of visual words (BoVW), Yottixel, SISH, RetCCL, and some of their potential variants. We analyze their algorithms and structures and assess their performance. For this evaluation, we utilized four internal datasets (1269 patients) and three public datasets (1207 patients), totaling more than 200,000 patches from 38 different classes/subtypes across five primary sites. Certain search engines, for example, BoVW, exhibit notable efficiency and speed but suffer from low accuracy. Conversely, search engines like Yottixel demonstrate efficiency and speed, providing moderately accurate results. Recent proposals, including SISH, display inefficiency and yield inconsistent outcomes, while alternatives like RetCCL prove inadequate in both accuracy and efficiency. Further research is imperative to address the dual aspects of accuracy and minimal storage requirements in histopathological image search.

On image search in histopathology

Pathology images of histopathology can be acquired from camera-mounted microscopes or whole-slide scanners. Utilizing similarity calculations to match patients based on these images holds significant potential in research and clinical contexts. Recent advancements in search technologies allow for implicit quantification of tissue morphology across diverse primary sites, facilitating comparisons, and enabling inferences about diagnosis, and potentially prognosis, and predictions for new patients when compared against a curated database of diagnosed and treated cases. In this article, we comprehensively review the latest developments in image search technologies for histopathology, offering a concise overview tailored for computational pathology researchers seeking effective, fast, and efficient image search methods in their work.

Multi-Magnification Image Search in Digital Pathology

This paper investigates the effect of magnification on content-based image search in digital pathology archives and proposes to use multi-magnification image representation. Image search in large archives of digital pathology slides provides researchers and medical professionals with an opportunity to match records of current and past patients and learn from evidently diagnosed and treated cases. When working with microscopes, pathologists switch between different magnification levels while examining tissue specimens to find and evaluate various morphological features. Inspired by the conventional pathology workflow, we have investigated several magnification levels in digital pathology and their combinations to minimize the gap between AI-enabled image search methods and clinical settings. The proposed searching framework does not rely on any regional annotation and potentially applies to millions of unlabelled (raw) whole slide images. This paper suggests two approaches for combining magnification levels and compares their performance. The first approach obtains a single-vector deep feature representation for a digital slide, whereas the second approach works with a multi-vector deep feature representation. We report the search results of 20×, 10×, and 5× magnifications and their combinations on a subset of The Cancer Genome Atlas (TCGA) repository. The experiments verify that cell-level information at the highest magnification is essential for searching for diagnostic purposes. In contrast, low-magnification information may improve this assessment depending on the tumor type. Our multi-magnification approach achieved up to 11% F1-score improvement in searching among the urinary tract and brain tumor subtypes compared to the single-magnification image search.

Fast and scalable search of whole-slide images via self-supervised deep learning

The adoption of digital pathology has enabled the curation of large repositories of gigapixel whole-slide images (WSIs). Computationally identifying WSIs with similar morphologic features within large repositories without requiring supervised training can have significant applications. However, the retrieval speeds of algorithms for searching similar WSIs often scale with the repository size, which limits their clinical and research potential. Here we show that self-supervised deep learning can be leveraged to search for and retrieve WSIs at speeds that are independent of repository size. The algorithm, which we named SISH (for self-supervised image search for histology) and provide as an open-source package, requires only slide-level annotations for training, encodes WSIs into meaningful discrete latent representations and leverages a tree data structure for fast searching followed by an uncertainty-based ranking algorithm for WSI retrieval. We evaluated SISH on multiple tasks (including retrieval tasks based on tissue-patch queries) and on datasets spanning over 22,000 patient cases and 56 disease subtypes. SISH can also be used to aid the diagnosis of rare cancer types for which the number of available WSIs is often insufficient to train supervised deep-learning models.

Deep Learning Approaches and Applications in Toxicologic Histopathology: Current Status and Future Perspectives

Whole slide imaging enables the use of a wide array of digital image analysis tools that are revolutionizing pathology. Recent advances in digital pathology and deep convolutional neural networks have created an enormous opportunity to improve workflow efficiency, provide more quantitative, objective, and consistent assessments of pathology datasets, and develop decision support systems. Such innovations are already making their way into clinical practice. However, the progress of machine learning - in particular, deep learning (DL) - has been rather slower in nonclinical toxicology studies. Histopathology data from toxicology studies are critical during the drug development process that is required by regulatory bodies to assess drug-related toxicity in laboratory animals and its impact on human safety in clinical trials. Due to the high volume of slides routinely evaluated, low-throughput, or narrowly performing DL methods that may work well in small-scale diagnostic studies or for the identification of a single abnormality are tedious and impractical for toxicologic pathology. Furthermore, regulatory requirements around good laboratory practice are a major hurdle for the adoption of DL in toxicologic pathology. This paper reviews the major DL concepts, emerging applications, and examples of DL in toxicologic pathology image analysis. We end with a discussion of specific challenges and directions for future research.

A Digital Pathology Solution to Resolve the Tissue Floater Conundrum

CONTEXT.—

Pathologists may encounter extraneous pieces of tissue (tissue floaters) on glass slides because of specimen cross-contamination. Troubleshooting this problem, including performing molecular tests for tissue identification if available, is time consuming and often does not satisfactorily resolve the problem.

OBJECTIVE.—

To demonstrate the feasibility of using an image search tool to resolve the tissue floater conundrum.

DESIGN.—

A glass slide was produced containing 2 separate hematoxylin and eosin (H&E)-stained tissue floaters. This fabricated slide was digitized along with the 2 slides containing the original tumors used to create these floaters. These slides were then embedded into a dataset of 2325 whole slide images comprising a wide variety of H&E stained diagnostic entities. Digital slides were broken up into patches and the patch features converted into barcodes for indexing and easy retrieval. A deep learning-based image search tool was employed to extract features from patches via barcodes, hence enabling image matching to each tissue floater.

RESULTS.—

There was a very high likelihood of finding a correct tumor match for the queried tissue floater when searching the digital database. Search results repeatedly yielded a correct match within the top 3 retrieved images. The retrieval accuracy improved when greater proportions of the floater were selected. The time to run a search was completed within several milliseconds.

CONCLUSIONS.—

Using an image search tool offers pathologists an additional method to rapidly resolve the tissue floater conundrum, especially for those laboratories that have transitioned to going fully digital for primary diagnosis.

Objective Diagnosis for Histopathological Images Based on Machine Learning Techniques: Classical Approaches and New Trends

Histopathology refers to the examination by a pathologist of biopsy samples. Histopathology images are captured by a microscope to locate, examine, and classify many diseases, such as different cancer types. They provide a detailed view of different types of diseases and their tissue status. These images are an essential resource with which to define biological compositions or analyze cell and tissue structures. This imaging modality is very important for diagnostic applications. The analysis of histopathology images is a prolific and relevant research area supporting disease diagnosis. In this paper, the challenges of histopathology image analysis are evaluated. An extensive review of conventional and deep learning techniques which have been applied in histological image analyses is presented. This review summarizes many current datasets and highlights important challenges and constraints with recent deep learning techniques, alongside possible future research avenues. Despite the progress made in this research area so far, it is still a significant area of open research because of the variety of imaging techniques and disease-specific characteristics.

Development of orthotopic tumour models using ultrasound-guided intrahepatic injection

Mouse models of human diseases are an essential part of the translational pipeline. Orthotopic tumour mouse models are increasingly being used in cancer research due to their increased clinical relevance over subcutaneous xenograft models, particularly in relation to metastatic disease. In this study, we have developed orthotopic colorectal cancer liver metastases (CRCLM) and primary cholangiocarcinoma (CCA) models in BALB/c nude mice using minimally invasive ultrasound-guided intrahepatic injection. Due to its minimally invasive nature, the method reduced risk from surgical complications whilst being fast and easy to perform and resulted in measurable tumour volumes 1 to 3 weeks post-injection. Tumour volumes were monitored in vivo by weekly high-frequency ultrasound (HF-US) and/or twice weekly bioluminescence imaging (BLI) and confirmed with end-point histology. Take rates were high for human CRC cells (>73%) and for CCA cells (90%). We have demonstrated that this method reliably induces CRCLM and CCAs, in which tumour volume can be monitored throughout using HF-US and/or BLI. This provides a promising experimental tool for future testing of cancer therapeutics in an orthotopic model.

Similar image search for histopathology: SMILY

The increasing availability of large institutional and public histopathology image datasets is enabling the searching of these datasets for diagnosis, research, and education. Although these datasets typically have associated metadata such as diagnosis or clinical notes, even carefully curated datasets rarely contain annotations of the location of regions of interest on each image. As pathology images are extremely large (up to 100,000 pixels in each dimension), further laborious visual search of each image may be needed to find the feature of interest. In this paper, we introduce a deep-learning-based reverse image search tool for histopathology images: Similar Medical Images Like Yours (SMILY). We assessed SMILY's ability to retrieve search results in two ways: using pathologist-provided annotations, and via prospective studies where pathologists evaluated the quality of SMILY search results. As a negative control in the second evaluation, pathologists were blinded to whether search results were retrieved by SMILY or randomly. In both types of assessments, SMILY was able to retrieve search results with similar histologic features, organ site, and prostate cancer Gleason grade compared with the original query. SMILY may be a useful general-purpose tool in the pathologist's arsenal, to improve the efficiency of searching large archives of histopathology images, without the need to develop and implement specific tools for each application.

Machine learning approaches for pathologic diagnosis

Machine learning techniques, especially deep learning techniques such as convolutional neural networks, have been successfully applied to general image recognitions since their overwhelming performance at the 2012 ImageNet Large Scale Visual Recognition Challenge. Recently, such techniques have also been applied to various medical, including histopathological, images to assist the process of medical diagnosis. In some cases, deep learning-based algorithms have already outperformed experienced pathologists for recognition of histopathological images. However, pathological images differ from general images in some aspects, and thus, machine learning of histopathological images requires specialized learning methods. Moreover, many pathologists are skeptical about the ability of deep learning technology to accurately recognize histopathological images because what the learned neural network recognizes is often indecipherable to humans. In this review, we first introduce various applications incorporating machine learning developed to assist the process of pathologic diagnosis, and then describe machine learning problems related to histopathological image analysis, and review potential ways to solve these problems.

Computer-Aided Laser Dissection: A Microdissection Workflow Leveraging Image Analysis Tools

Introduction

The development and application of new molecular diagnostic assays based on next-generation sequencing and proteomics require improved methodologies for procurement of target cells from histological sections. Laser microdissection can successfully isolate distinct cells from tissue specimens based on visual selection for many research and clinical applications. However, this can be a daunting task when a large number of cells are required for molecular analysis or when a sizeable number of specimens need to be evaluated.

Materials and Methods

To improve the efficiency of the cellular identification process, we describe a microdissection workflow that leverages recently developed and open source image analysis algorithms referred to as computer-aided laser dissection (CALD). CALD permits a computer algorithm to identify the cells of interest and drive the dissection process.

Results

We describe several "use cases" that demonstrate the integration of image analytic tools probabilistic pairwise Markov model, ImageJ, spatially invariant vector quantization (SIVQ), and eSeg onto the ThermoFisher Scientific ArcturusXT and Leica LMD7000 microdissection platforms.

Conclusions

The CALD methodology demonstrates the integration of image analysis tools with the microdissection workflow and shows the potential impact to clinical and life science applications.

Machine Learning Methods for Histopathological Image Analysis

Abundant accumulation of digital histopathological images has led to the increased demand for their analysis, such as computer-aided diagnosis using machine learning techniques. However, digital pathological images and related tasks have some issues to be considered. In this mini-review, we introduce the application of digital pathological image analysis using machine learning algorithms, address some problems specific to such analysis, and propose possible solutions.

Evaluating stability of histomorphometric features across scanner and staining variations: prostate cancer diagnosis from whole slide images

Quantitative histomorphometry (QH) is the process of computerized feature extraction from digitized tissue slide images to predict disease presence, behavior, and outcome. Feature stability between sites may be compromised by laboratory-specific variables including dye batch, slice thickness, and the whole slide scanner used. We present two new measures, preparation-induced instability score and latent instability score, to quantify feature instability across and within datasets. In a use case involving prostate cancer, we examined QH features which may detect cancer on whole slide images. Using our method, we found that five feature families (graph, shape, co-occurring gland tensor, sub-graph, and texture) were different between datasets in 19.7% to 48.6% of comparisons while the values expected without site variation were 4.2% to 4.6%. Color normalizing all images to a template did not reduce instability. Scanning the same 34 slides on three scanners demonstrated that Haralick features were most substantively affected by scanner variation, being unstable in 62% of comparisons. We found that unstable feature families performed significantly worse in inter- than intrasite classification. Our results appear to suggest QH features should be evaluated across sites to assess robustness, and class discriminability alone should not represent the benchmark for digital pathology feature selection.

Multi-Pass Adaptive Voting for Nuclei Detection in Histopathological Images

Nuclei detection is often a critical initial step in the development of computer aided diagnosis and prognosis schemes in the context of digital pathology images. While over the last few years, a number of nuclei detection methods have been proposed, most of these approaches make idealistic assumptions about the staining quality of the tissue. In this paper, we present a new Multi-Pass Adaptive Voting (MPAV) for nuclei detection which is specifically geared towards images with poor quality staining and noise on account of tissue preparation artifacts. The MPAV utilizes the symmetric property of nuclear boundary and adaptively selects gradient from edge fragments to perform voting for a potential nucleus location. The MPAV was evaluated in three cohorts with different staining methods: Hematoxylin &Eosin, CD31 &Hematoxylin, and Ki-67 and where most of the nuclei were unevenly and imprecisely stained. Across a total of 47 images and nearly 17,700 manually labeled nuclei serving as the ground truth, MPAV was able to achieve a superior performance, with an area under the precision-recall curve (AUC) of 0.73. Additionally, MPAV also outperformed three state-of-the-art nuclei detection methods, a single pass voting method, a multi-pass voting method, and a deep learning based method.