Detection and Classification of Cancer from Microscopic Biopsy Images Using Clinically Significant and Biologically Interpretable Features

Kumar, Rajesh; Srivastava, Rajeev; Srivastava, S. P.

doi:10.1155/2015/457906

Cited by 185 publications

(69 citation statements)

References 37 publications

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“…Classical machine learning models were fit using implementations provided in the R programming environment (R Foundation) in order to predict cell type based on cell features. Two models, linear Support Vector Machine (LSVM)31 and Random Forests (RF)32, were chosen based on their popularity in a number of classification tasks, including cell classification in microscopy images3334. In contrast to the two previous models, ConvNets directly learns representations from images, bypassing the need to manually define features.…”

Section: Resultsmentioning

confidence: 99%

Relevance of deep learning to facilitate the diagnosis of HER2 status in breast cancer

Vandenberghe

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et al. 2017

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Tissue biomarker scoring by pathologists is central to defining the appropriate therapy for patients with cancer. Yet, inter-pathologist variability in the interpretation of ambiguous cases can affect diagnostic accuracy. Modern artificial intelligence methods such as deep learning have the potential to supplement pathologist expertise to ensure constant diagnostic accuracy. We developed a computational approach based on deep learning that automatically scores HER2, a biomarker that defines patient eligibility for anti-HER2 targeted therapies in breast cancer. In a cohort of 71 breast tumour resection samples, automated scoring showed a concordance of 83% with a pathologist. The twelve discordant cases were then independently reviewed, leading to a modification of diagnosis from initial pathologist assessment for eight cases. Diagnostic discordance was found to be largely caused by perceptual differences in assessing HER2 expression due to high HER2 staining heterogeneity. This study provides evidence that deep learning aided diagnosis can facilitate clinical decision making in breast cancer by identifying cases at high risk of misdiagnosis.

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Section: Resultsmentioning

confidence: 99%

Relevance of deep learning to facilitate the diagnosis of HER2 status in breast cancer

Vandenberghe

Scott

Scorer

et al. 2017

Sci Rep

170

109

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“…We used the described watershed segmentation algorithm to separate the overlapping cell nuclei. This has been used previously for nucleus counting and to extract features for classification [23]. Figure 4 shows the necessary steps for watershed segmentation, including segmenting the nuclei image, converting to a binary image, applying the Euclidean distance transform, and labeling the watershed image using color mapping.…”

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confidence: 99%

Quantitative Analysis of Benign and Malignant Tumors in Histopathology: Predicting Prostate Cancer Grading Using SVM

et al. 2019

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An adenocarcinoma is a type of malignant cancerous tissue that forms from a glandular structure in epithelial tissue. Analyzed stained microscopic biopsy images were used to perform image manipulation and extract significant features for support vector machine (SVM) classification, to predict the Gleason grading of prostate cancer (PCa) based on the morphological features of the cell nucleus and lumen. Histopathology biopsy tissue images were used and categorized into four Gleason grade groups, namely Grade 3, Grade 4, Grade 5, and benign. The first three grades are considered malignant. K-means and watershed algorithms were used for color-based segmentation and separation of overlapping cell nuclei, respectively. In total, 400 images, divided equally among the four groups, were collected for SVM classification. To classify the proposed morphological features, SVM classification based on binary learning was performed using linear and Gaussian classifiers. The prediction model yielded an accuracy of 88.7% for malignant vs. benign, 85.0% for Grade 3 vs. Grade 4, 5, and 92.5% for Grade 4 vs. Grade 5. The SVM, based on biopsy-derived image features, consistently and accurately classified the Gleason grading of prostate cancer. All results are comparatively better than those reported in the literature. Appl. Sci. 2019, 9, 2969 2 of 17 practitioners, for both diagnosis and treatment. Usually, the cancer detection process in histopathology consists of categorizing stained microscopic biopsy images into malignant and benign.The Gleason grade grouping system defines Gleason scores ≤ 6 as grade 1, score 3 + 4 = 7 as grade 2, score 4 + 3 = 7 as grade 3, score 4 + 4, 3 + 5 or 5 + 3 = 8 as grade 4, and score 4 + 5, 5 + 4 or 5 + 5 = 9 or 10 as grade 5. The Gleason score is obtained by adding the primary (most common) and secondary (second most common) scores from H&E stained tissue microscopic images. This system was developed by Dr. Donald F Gleason, who was a Pathologist in Minnesota, and members of the Veterans Administration Cooperative Urological Research Group (VACURG) [3]. This system was tested on a large number of patients, including long-term follow-ups and is considered an outstanding success.In recent years, an excellent and important addition to microscopy and digital imaging has been developed for microscopes that are used to convert stained tissue slides into whole slide digital images. This allows for more efficient computer-based viewing and analysis of histopathology. Early diagnosis and treatment are required, to avoid the enlargement of cancer cells in the prostate gland and control the spreading of more aggressive tumors to other parts of the body.The digital pathology field has grown dramatically over recent years, largely due to technological advancements in image processing and machine learning algorithms, and increases in computational power. As part of this field, many methods have been proposed for automatic histopathological image analysis and classification. In this paper, color segmentation, based...

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“…Malignant cells have been reported to develop abnormal, irregularly shaped nuclei [14,15]. To separate and label benign and malignant tissues, morphologic features, such as gray-level texture features, color-based features, Law's Texture Energy-based features, Tamura's features, and wavelet features, have been applied [16][17][18][19][20]. These texture-based methods consider the neighborhood of cells, applying the gray scale co-occurrence matrix, the wavelet transformation, and Fourier transformation, see [21] for a detailed overview.…”

Section: Introductionmentioning

confidence: 99%

Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma

et al. 2020

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In pathology, tissue images are evaluated using a light microscope, relying on the expertise and experience of pathologists. There is a great need for computational methods to quantify and standardize histological observations. Computational quantification methods become more and more essential to evaluate tissue images. In particular, the distribution of tumor cells and their microenvironment are of special interest. Here, we systematically investigated tumor cell properties and their spatial neighborhood relations by a new application of statistical analysis to whole slide images of Hodgkin lymphoma, a tumor arising in lymph nodes, and inflammation of lymph nodes called lymphadenitis. We considered properties of more than 400, 000 immunohistochemically stained, CD30-positive cells in 35 whole slide images of tissue sections from subtypes of the classical Hodgkin lymphoma, nodular sclerosis and mixed cellularity, as well as from lymphadenitis. We found that cells of specific morphology exhibited significantly favored and unfavored spatial neighborhood relations of cells in dependence of their morphology. This information is important to evaluate differences between Hodgkin lymph nodes infiltrated by tumor cells (Hodgkin lymphoma) and inflamed lymph nodes, concerning the neighborhood relations of cells and the sizes of cells. The quantification of neighborhood relations revealed new insights of relations of CD30-positive cells in different diagnosis cases. The approach is general and can easily be applied to whole slide image analysis of other tumor types.PLOS Computational Biology | https://doi.In pathology, histological diagnosis is still challenging, in particular, for tumor diseases. Pathologists diagnose the disease and its stage of development on the basis of evaluation and interpretation of images of tissue sections. The quantification of experimental data to support decisions of diagnosis and prognosis, applying bioinformatics methods, is an important issue. Here, we introduce a new, general approach to analyze tissue images of tumor and non-tumor patients and to evaluate the distribution of tumor cells in the tissue. Moreover, we consider neighborhood relations between immunostained cells of different cell morphology. We focus on a special type of lymph node tumor, the Hodgkin lymphoma, exploring the two main types of the classical Hodgkin lymphoma, the nodular sclerosis and the mixed cellularity, and the non-tumor case, the lymphadenitis, representing an inflammation of the lymph node. We considered more than 400, 000 cells immunohistochemically stained with CD30 in 35 whole slide images of tissue sections. We found that cells of specific morphology exhibited significant relations to cells of certain morphology as spatial nearest neighbor. We could show different neighborhood patterns of CD30-positive cells between tumor and non-tumor. The approach is general and can easily be applied to other tumor types.

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Detection and Classification of Cancer from Microscopic Biopsy Images Using Clinically Significant and Biologically Interpretable Features

Cited by 185 publications

References 37 publications

Relevance of deep learning to facilitate the diagnosis of HER2 status in breast cancer

Relevance of deep learning to facilitate the diagnosis of HER2 status in breast cancer

Quantitative Analysis of Benign and Malignant Tumors in Histopathology: Predicting Prostate Cancer Grading Using SVM

Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma

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