CA : A Cancer Journal for Clinicians

Over recent years, deep learning (DL) has established itself as a powerful tool across a broad spectrum of domains in imaging—e [...]

https://www.mdpi.com/2313-433X/7/4/74/pdf

Deep Learning in Medical Image Analysis.

The process of image segmentation is partitioning an image into its constituent parts and is a significant approach for extracting interesting features from images. Over a couple of decades, many efficient image segmentation approaches have been formulated for various applications. Still, it is a challenging and complex issue, especially for color image segmentation. To moderate this difficulty, a novel multilevel thresholding approach is proposed in this paper based on the electromagnetism optimization (EMO) technique with an energy curve, named multilevel thresholding based on EMO and energy curve (MTEMOE). To compute the optimized threshold values, Otsu’s variance and Kapur’s entropy are deployed as fitness functions; both values should be maximized to locate optimal threshold values. In both Kapur’s and Otsu’s methods, the pixels of an image are classified into different classes based on the threshold level selected on the histogram. Optimal threshold levels give higher efficiency of segmentation; the EMO technique is used to find optimal thresholds in this research. The methods based on an image’s histograms do not possess the spatial contextual information for finding the optimal threshold levels. To abolish this deficiency an energy curve is used instead of the histogram and this curve can establish the spatial relationship of pixels with their neighbor pixels. To study the experimental results of the proposed scheme, several color benchmark images are considered at various threshold levels and compared with other meta-heuristic algorithms: multi-verse optimization, whale optimization algorithm, and so on. The investigational results are illustrated in terms of mean square error, peak signal-to-noise ratio, the mean value of fitness reach, feature similarity, structural similarity, variation of information, and probability rand index. The results reveal that the proposed MTEMOE approach overtops other state-of-the-art algorithms to solve engineering problems in various fields.

/pdf/efficient-approach-to-color-image-segmentation-based-on-3us11n71.pdf

Efficient Approach to Color Image Segmentation Based on Multilevel Thresholding Using EMO Algorithm by Considering Spatial Contextual Information

Breast cancer remains a highly prevalent disease with considerable inter- and intra-tumoral heterogeneity complicating prognostication and treatment decisions. The utilization and depth of genomic, transcriptomic and proteomic data for cancer has exploded over recent times and the addition of spatial context to this information, by understanding the correlating morphologic and spatial patterns of cells in tissue samples, has created an exciting frontier of research, histo-genomics. At the same time, deep learning (DL), a class of machine learning algorithms employing artificial neural networks, has rapidly progressed in the last decade with a confluence of technical developments - including the advent of modern graphic processing units (GPU), allowing efficient implementation of increasingly complex architectures at scale; advances in the theoretical and practical design of network architectures; and access to larger datasets for training - all leading to sweeping advances in image classification and object detection. In this review, we examine recent developments in the application of DL in breast cancer histology with particular emphasis of those producing biologic insights or novel biomarkers, spanning the extraction of genomic information to the use of stroma to predict cancer recurrence, with the aim of suggesting avenues for further advancing this exciting field. 

/pdf/biological-insights-and-novel-biomarker-discovery-through-2or7v1sk.pdf

Biological insights and novel biomarker discovery through deep learning approaches in breast cancer histopathology

This paper describes a methodology that extracts key morphological features from histological breast cancer images in order to automatically assess Tumour Cellularity (TC) in Neo-Adjuvant treatment (NAT) patients. The response to NAT gives information on therapy efficacy and it is measured by the residual cancer burden index, which is composed of two metrics: TC and the assessment of lymph nodes. The data consist of whole slide images (WSIs) of breast tissue stained with Hematoxylin and Eosin (H&E) released in the 2019 SPIE Breast Challenge. The methodology proposed is based on traditional computer vision methods (K-means, watershed segmentation, Otsu’s binarisation, and morphological operations), implementing colour separation, segmentation, and feature extraction. Correlation between morphological features and the residual TC after a NAT treatment was examined. Linear regression and statistical methods were used and twenty-two key morphological parameters from the nuclei, epithelial region, and the full image were extracted. Subsequently, an automated TC assessment that was based on Machine Learning (ML) algorithms was implemented and trained with only selected key parameters. The methodology was validated with the score assigned by two pathologists through the intra-class correlation coefficient (ICC). The selection of key morphological parameters improved the results reported over other ML methodologies and it was very close to deep learning methodologies. These results are encouraging, as a traditionally-trained ML algorithm can be useful when limited training data are available preventing the use of deep learning approaches.

Morphological Estimation of Cellularity on Neo-Adjuvant Treated Breast Cancer Histological Images.

This paper describes a methodology that extracts morphological features from histological breast cancer images stained for Hematoxilyn and Eosin (H&E). Cellularity was estimated and the correlation between features and the residual tumour size cellularity after a Neo-Adjuvant treatment (NAT) was examined. Images from whole slide imaging (WSI) were processed automatically with traditional computer vision methods to extract twenty two morphological parameters from the nuclei, epithelial region and the global image. The methodology was applied to a set of images from breast cancer under NAT. The data came from the BreastPathQ Cancer Cellularity Challenge 2019, and consisted of 2579 patches of 255×255 pixels of H&E histopatological samples from NAT treatment patients. The methodology automatically implements colour separation, segmentation and morphological analysis using traditional algorithms (K-means grouping, watershed segmentation, Otsu’s binarisation). Linear regression methods were applied to determine strongest correlation between the parameters and the cancer cellularity. The morphological parameters showed correlation with the residual tumour cancer cellularity. The strongest correlations corresponded to the stroma concentration value (r = −0.9786) and value from HSV image colour space (r = −0.9728), both from a global image parameters.

https://www.biorxiv.org/content/biorxiv/early/2020/04/03/2020.04.01.020719.full.pdf

Morphological estimation of Cellularity on Neo-adjuvant treated breast cancer histological images

This paper describes a method for residual tumour cellularity (TC) estimation in Neoadjuvant treatment (NAT) of advanced breast cancer. This is determined manually by visual inspection by a radiologist, then an automated computation will contribute to reduce time workload and increase precision and accuracy. TC is estimated as the ratio of tumour area by total image area estimated after the NAT. The method proposed computes TC by using machine learning techniques trained with information on morphological parameters of segmented nuclei in order to classify regions of the image as tumour or normal. The data is provided by the 2019 SPIE Breast challenge, which was proposed to develop automated TC computation algorithms. Three algorithms were implemented: Support Vector Machines, Nearest K-means and Adaptive Boosting (AdaBoost) decision trees. Performance based on accuracy is compared and evaluated and the best result was obtained with Support Vector Machines. Results obtained by the methods implemented were submitted during ongoing challenge with a maximum of 0.76 of prediction probability of success.

/pdf/estimation-of-cellularity-in-tumours-treated-with-4x0gsabgoj.pdf

Estimation of cellularity in tumours treated with Neoadjuvant therapy: A comparison of Machine Learning algorithms

Mexico is a country prone to catastrophic events of seismic, vulcanological or meteorological origin, among others. For this reason, many organizations monitor in Mexico different areas to prevent catastrophes. The Emergency Alert Systems (EAS) advise about the advent of a possible catastrophic event to the population in general. This paper explores the EAS in Mexico in order to propose improvements. First, the characteristics of the existing Emergency Alert Systems in México are evaluated. As the broadcasting have traditionally been the main alert media for the population, the coverage of radio and television is studied in order to know whether it is enough to cover all the country. Finally, a new integral Emergency Alert System covering all the country is proposed.

Victor García Garduño

Papers

Morphological Estimation of Cellularity on Neo-Adjuvant Treated Breast Cancer Histological Images.

Morphological estimation of Cellularity on Neo-adjuvant treated breast cancer histological images

Estimation of cellularity in tumours treated with Neoadjuvant therapy: A comparison of Machine Learning algorithms

An Integral Emergency Alert System for Mexico