Analytical Approaches for the Segmentation of the Zebrafish Brain Vasculature.

With advancements in imaging techniques, data visualization allows new insights into fundamental biological processes of development and disease. However, although biomedical science is heavily reliant on imaging data, interpretation of datasets is still often based on subjective visual assessment rather than rigorous quantitation. This overview presents steps to validate image processing and segmentation using the zebrafish brain vasculature data acquired with light sheet fluorescence microscopy as a use case. Blood vessels are of particular interest to both medical and biomedical science. Specific image enhancement filters have been developed that enhance blood vessels in imaging data prior to segmentation. Using the Sato enhancement filter as an example, we discuss how filter application can be evaluated and optimized. Approaches from the medical field such as simulated, experimental, and augmented datasets can be used to gain the most out of the data at hand. Using such datasets, we provide an overview of how biologists and data analysts can assess the accuracy, sensitivity, and robustness of their segmentation approaches that allow extraction of objects from images. Importantly, even after optimization and testing of a segmentation workflow (e.g., from a particular reporter line to another or between immunostaining processes), its generalizability is often limited, and this can be tested using double-transgenic reporter lines. Lastly, due to the increasing importance of deep learning networks, a comparative approach can be adopted to study their applicability to biological datasets. In summary, we present a broad methodological overview ranging from image enhancement to segmentation with a mixed approach of experimental, simulated, and augmented datasets to assess and validate vascular segmentation using the zebrafish brain vasculature as an example. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. HIGHLIGHTS: Simulated, experimental, and augmented datasets provide an alternative to overcome the lack of segmentation gold standards and phantom models for zebrafish cerebrovascular segmentation. Direct generalization of a segmentation approach to the data for which it was not optimized (e.g., different transgenics or antibody stainings) should be treated with caution. Comparison of different deep learning segmentation methods can be used to assess their applicability to data. Here, we show that the zebrafish cerebral vasculature can be segmented with U-Net-based architectures, which outperform SegNet architectures.

Single-Input Multi-Output U-Net for Automated 2D Foetal Brain Segmentation of MR Images.

In this work, we develop the Single-Input Multi-Output U-Net (SIMOU-Net), a hybrid network for foetal brain segmentation inspired by the original U-Net fused with the holistically nested edge detection (HED) network. The SIMOU-Net is similar to the original U-Net but it has a deeper architecture and takes account of the features extracted from each side output. It acts similar to an ensemble neural network, however, instead of averaging the outputs from several independently trained models, which is computationally expensive, our approach combines outputs from a single network to reduce the variance of predications and generalization errors. Experimental results using 200 normal foetal brains consisting of over 11,500 2D images produced Dice and Jaccard coefficients of 94.2 ± 5.9% and 88.7 ± 6.9%, respectively. We further tested the proposed network on 54 abnormal cases (over 3500 images) and achieved Dice and Jaccard coefficients of 91.2 ± 6.8% and 85.7 ± 6.6%, respectively.

Status and Recommendations of Technological and Data-Driven Innovations in Cancer Care: Focus Group Study.

BACKGROUND: The status of the data-driven management of cancer care as well as the challenges, opportunities, and recommendations aimed at accelerating the rate of progress in this field are topics of great interest. Two international workshops, one conducted in June 2019 in Cordoba, Spain, and one in October 2019 in Athens, Greece, were organized by four Horizon 2020 (H2020) European Union (EU)-funded projects: BOUNCE, CATCH ITN, DESIREE, and MyPal. The issues covered included patient engagement, knowledge and data-driven decision support systems, patient journey, rehabilitation, personalized diagnosis, trust, assessment of guidelines, and interoperability of information and communication technology (ICT) platforms. A series of recommendations was provided as the complex landscape of data-driven technical innovation in cancer care was portrayed. OBJECTIVE: This study aims to provide information on the current state of the art of technology and data-driven innovations for the management of cancer care through the work of four EU H2020-funded projects. METHODS: Two international workshops on ICT in the management of cancer care were held, and several topics were identified through discussion among the participants. A focus group was formulated after the second workshop, in which the status of technological and data-driven cancer management as well as the challenges, opportunities, and recommendations in this area were collected and analyzed. RESULTS: Technical and data-driven innovations provide promising tools for the management of cancer care. However, several challenges must be successfully addressed, such as patient engagement, interoperability of ICT-based systems, knowledge management, and trust. This paper analyzes these challenges, which can be opportunities for further research and practical implementation and can provide practical recommendations for future work. CONCLUSIONS: Technology and data-driven innovations are becoming an integral part of cancer care management. In this process, specific challenges need to be addressed, such as increasing trust and engaging the whole stakeholder ecosystem, to fully benefit from these innovations.

Breast density classification in mammograms: An investigation of encoding techniques in binary-based local patterns.

We investigate various channel encoding techniques applied to breast density classification in mammograms; specifically, local binary, ternary, and quinary encoding approaches are considered. Subsequently, we propose a new encoding approach based on a seven-encoding technique, yielding a new local pattern operator called a local septenary pattern operator. Experimental results suggest that the proposed local pattern operator is robust and outperforms the other encoding techniques when evaluated on the Mammographic Image Analysis Society (MIAS) and InBreast datasets. The local septenary pattern operator achieved a maximum classification accuracy of 83.3% and 80.5% on the MIAS and InBreast datasets, respectively. The closest comparison achieved by the other local pattern operators is the local quinary operator, with maximum accuracies of 82.1% (MIAS) and 80.1% (InBreast), respectively.

Breast pectoral muscle segmentation in mammograms using a modified holistically-nested edge detection network.

This paper presents a method for automatic breast pectoral muscle segmentation in mediolateral oblique mammograms using a Convolutional Neural Network (CNN) inspired by the Holistically-nested Edge Detection (HED) network. Most of the existing methods in the literature are based on hand-crafted models such as straight-line, curve-based techniques or a combination of both. Unfortunately, such models are insufficient when dealing with complex shape variations of the pectoral muscle boundary and when the boundary is unclear due to overlapping breast tissue. To compensate for these issues, we propose a neural network framework that incorporates multi-scale and multi-level learning, capable of learning complex hierarchical features to resolve spatial ambiguity in estimating the pectoral muscle boundary. For this purpose, we modified the HED network architecture to specifically find 'contour-like' objects in mammograms. The proposed framework produced a probability map that can be used to estimate the initial pectoral muscle boundary. Subsequently, we process these maps by extracting morphological properties to find the actual pectoral muscle boundary. Finally, we developed two different post-processing steps to find the actual pectoral muscle boundary. Quantitative evaluation results show that the proposed method is comparable with alternative state-of-the-art methods producing on average values of 94.8 ±â€¯8.5% and 97.5 ±â€¯6.3% for the Jaccard and Dice similarity metrics, respectively, across four different databases.

Segmentation of breast MR images using a generalised 2D mathematical model with inflation and deflation forces of active contours.

In medical computer aided diagnosis systems, image segmentation is one of the major pre-processing steps used to ensure only the region of interest, such as the breast region, will be processed in subsequent steps. Nevertheless, breast segmentation is a difficult task due to low contrast and inhomogeneity, especially when estimating the chest wall in magnetic resonance (MR) images. In fact, the chest wall comprises fat, skin, muscles, and the thoracic skeleton, which can misguide automatic methods when attempting to estimate its location. The objective of the study is to develop a fully automated method for breast and pectoral muscle boundary estimation in MR images. Firstly, we develop a 2D breast mathematical model based on 30 MRI slices (from a patient) and identify important landmarks to obtain a model for the general shape of the breast in an axial plane. Subsequently, we use Otsu's thresholding approach and Canny edge detection to estimate the breast boundary. The active contour method is then employed using both inflation and deflation forces to estimate the pectoral muscle boundary by taking account of information obtained from the proposed 2D model. Finally, the estimated boundary is smoothed using a median filter to remove outliers. Our two datasets contain 60 patients in total and the proposed method is evaluated based on 59 patients (one patient is used to develop the 2D breast model). On the first dataset (9 patients) the proposed method achieved Jaccard = 81.1% ±6.1 % and dice coefficient= 89.4% ±4.1 % and on the second dataset (50 patients) Jaccard = 84.9% ±5.8 % and dice coefficient = 92.3% ±3.6 %. These results are qualitatively comparable with the existing methods in the literature.

Deep learning in mammography and breast histology, an overview and future trends.

Recent improvements in biomedical image analysis using deep learning based neural networks could be exploited to enhance the performance of Computer Aided Diagnosis (CAD) systems. Considering the importance of breast cancer worldwide and the promising results reported by deep learning based methods in breast imaging, an overview of the recent state-of-the-art deep learning based CAD systems developed for mammography and breast histopathology images is presented. In this study, the relationship between mammography and histopathology phenotypes is described, which takes biological aspects into account. We propose a computer based breast cancer modelling approach: the Mammography-Histology-Phenotype-Linking-Model, which develops a mapping of features/phenotypes between mammographic abnormalities and their histopathological representation. Challenges are discussed along with the potential contribution of such a system to clinical decision making and treatment management.

A hierarchical pipeline for breast boundary segmentation and calcification detection in mammograms.

Breast cancer is one of the most common cancer risks to women in the world. Amongst multiple breast imaging modalities, mammography has been widely used in breast cancer diagnosis and screening. Quantitative analyses including breast boundary segmentation and calcification localization are essential steps in a Computer Aided Diagnosis system based on mammography analysis. Due to uneven signal spatial distributions of pectoral muscle and glandular tissue, plus various artifacts in imaging, it is still challenging to automatically analyze mammogram images with high precision. In this paper, a fully automated pipeline of mammogram image processing is proposed, which estimates skin-air boundary using gradient weight map, detects pectoral-breast boundary by unsupervised pixel-wise labeling with no pre-labeled areas needed, and finally detects calcifications inside the breast region with a novel texture filter. Experimental results on Mammogram Image Analysis Society database show that the proposed method performs breast boundary segmentation and calcification detection with high accuracy of 97.08% and 96.15% respectively, and slightly higher accuracies are achieved on Full-Field Digital Mammography image datasets. Calculation of Jaccard and Dice indexes between segmented breast regions and the ground truths are also included as comprehensive similarity evaluations, which could provide valuable support for mammogram analysis in clinic.

Fully automated breast boundary and pectoral muscle segmentation in mammograms.

Breast and pectoral muscle segmentation is an essential pre-processing step for the subsequent processes in computer aided diagnosis (CAD) systems. Estimating the breast and pectoral boundaries is a difficult task especially in mammograms due to artifacts, homogeneity between the pectoral and breast regions, and low contrast along the skin-air boundary. In this paper, a breast boundary and pectoral muscle segmentation method in mammograms is proposed. For breast boundary estimation, we determine the initial breast boundary via thresholding and employ Active Contour Models without edges to search for the actual boundary. A post-processing technique is proposed to correct the overestimated boundary caused by artifacts. The pectoral muscle boundary is estimated using Canny edge detection and a pre-processing technique is proposed to remove noisy edges. Subsequently, we identify five edge features to find the edge that has the highest probability of being the initial pectoral contour and search for the actual boundary via contour growing. The segmentation results for the proposed method are compared with manual segmentations using 322, 208 and 100mammograms from the Mammographic Image Analysis Society (MIAS), INBreast and Breast Cancer Digital Repository (BCDR) databases, respectively. Experimental results show that the breast boundary and pectoral muscle estimation methods achieved dice similarity coefficients of 98.8% and 97.8% (MIAS), 98.9% and 89.6% (INBreast) and 99.2% and 91.9% (BCDR), respectively.

Computer aided diagnosis of prostate cancer: A texton based approach.

PURPOSE: In this paper the authors propose a texton based prostate computer aided diagnosis approach which bypasses the typical feature extraction process such as filtering and convolution which can be computationally expensive. The study focuses the peripheral zone because 75% of prostate cancers start within this region and the majority of prostate cancers arising within this region are more aggressive than those arising in the transitional zone. METHODS: For the model development, square patches were extracted at random locations from malignant and benign regions. Subsequently, extracted patches were aggregated and clustered using k-means clustering to generate textons that represent both regions. All textons together form a texton dictionary, which was used to construct a texton map for every peripheral zone in the training images. Based on the texton map, histogram models for each malignant and benign tissue samples were constructed and used as a feature vector to train our classifiers. In the testing phase, four machine learning algorithms were employed to classify each unknown sample tissue based on its corresponding feature vector. RESULTS: The proposed method was tested on 418 T2-W MR images taken from 45 patients. Evaluation results show that the best three classifiers were Bayesian network (Az = 92.8% ± 5.9%), random forest (89.5% ± 7.1%), and k-NN (86.9% ± 7.5%). These results are comparable to the state-of-the-art in the literature. CONCLUSIONS: The authors have developed a prostate computer aided diagnosis method based on textons using a single modality of T2-W MRI without the need for the typical feature extraction methods, such as filtering and convolution. The proposed method could form a solid basis for a multimodality magnetic resonance imaging based systems.

Computer-aided detection of prostate cancer in T2-weighted MRI within the peripheral zone.

In this paper we propose a prostate cancer computer-aided diagnosis (CAD) system and suggest a set of discriminant texture descriptors extracted from T2-weighted MRI data which can be used as a good basis for a multimodality system. For this purpose, 215 texture descriptors were extracted and eleven different classifiers were employed to achieve the best possible results. The proposed method was tested based on 418 T2-weighted MR images taken from 45 patients and evaluated using 9-fold cross validation with five patients in each fold. The results demonstrated comparable results to existing CAD systems using multimodality MRI. We achieved an area under the receiver operating curve (A z ) values equal to [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] for Bayesian networks, ADTree, random forest and multilayer perceptron classifiers, respectively, while a meta-voting classifier using average probability as a combination rule achieved [Formula: see text].

Computer-aided diagnosis: detection and localization of prostate cancer within the peripheral zone.

We propose a methodology for prostate cancer detection and localization within the peripheral zone based on combining multiple segmentation techniques. We extract four image features using Gaussian and median filters. Subsequently, we use each image feature separately to generate binary segmentations. Finally, we take the intersection of all four binary segmentations, incorporating a model of the peripheral zone, and perform erosion to remove small false-positive regions. The initial evaluation of this method is based on 275 MRI images from 37 patients, and 86% of the slices were classified correctly with 87% and 86% sensitivity and specificity achieved, respectively. This paper makes two contributions: firstly, a novel computer-aided diagnosis approach, which is based on combining multiple segmentation techniques using only a small number of simple image features, and secondly, the development of the proposed method and its application in prostate cancer detection and localization using a single MRI modality with the results comparable with the state-of-the-art multimodality and advanced computer vision methods in the literature. Copyright © 2015 John Wiley & Sons, Ltd.