Locality sensitive deep learning for detection and classification of nuclei in routine colon cancer histology images

Detection and classification of cell nuclei in histopathology images of cancerous tissue stained with the standard hematoxylin and eosin stain is a challenging task due to cellular heterogeneity. Deep learning approaches have been shown to produce encouraging results on histopathology images in various studies. In this paper, we propose a Spatially Constrained Convolutional Neural Network (SC-CNN) to perform nucleus detection. SC-CNN regresses the likelihood of a pixel being the center of a nucleus, where high probability values are spatially constrained to locate in the vicinity of the center of nuclei. For classification of nuclei, we propose a novel Neighboring Ensemble Predictor (NEP) coupled with CNN to more accurately predict the class label of detected cell nuclei. The proposed approaches for detection and classification do not require segmentation of nuclei. We have evaluated them on a large dataset of colorectal adenocarcinoma images, consisting of more than 20,000 annotated nuclei belonging to four different classes. Our results show that the joint detection and classification of the proposed SC-CNN and NEP produces the highest average F1 score as compared to other recently published approaches. Prospectively, the proposed methods could offer benefit to pathology practice in terms of quantitative analysis of tissue constituents in whole-slide images, and could potentially lead to a better understanding of cancer

RCCNet: An Efficient Convolutional Neural Network for Histological Routine Colon Cancer Nuclei Classification

Efficient and precise classification of histological cell nuclei is of utmost importance due to its potential applications in the field of medical image analysis. It would facilitate the medical practitioners to better understand and explore various factors for cancer treatment. The classification of histological cell nuclei is a challenging task due to the cellular heterogeneity. This paper proposes an efficient Convolutional Neural Network (CNN) based architecture for classification of histological routine colon cancer nuclei named as RCCNet. The main objective of this network is to keep the CNN model as simple as possible. The proposed RCCNet model consists of only 1,512,868 learnable parameters which are significantly less compared to the popular CNN models such as AlexNet, CIFARVGG, GoogLeNet, and WRN. The experiments are conducted over publicly available routine colon cancer histological dataset "CRCHistoPhenotypes". The results of the proposed RCCNet model are compared with five state-of-the-art CNN models in terms of the accuracy, weighted average F1 score and training time. The proposed method has achieved a classification accuracy of 80.61% and 0.7887 weighted average F1 score. The proposed RCCNet is more efficient and generalized terms of the training time and data over-fitting, respectively.Comment: Published in ICARCV 201

MILD-Net: Minimal Information Loss Dilated Network for Gland Instance Segmentation in Colon Histology Images

The analysis of glandular morphology within colon histopathology images is an important step in determining the grade of colon cancer. Despite the importance of this task, manual segmentation is laborious, time-consuming and can suffer from subjectivity among pathologists. The rise of computational pathology has led to the development of automated methods for gland segmentation that aim to overcome the challenges of manual segmentation. However, this task is non-trivial due to the large variability in glandular appearance and the difficulty in differentiating between certain glandular and non-glandular histological structures. Furthermore, a measure of uncertainty is essential for diagnostic decision making. To address these challenges, we propose a fully convolutional neural network that counters the loss of information caused by max-pooling by re-introducing the original image at multiple points within the network. We also use atrous spatial pyramid pooling with varying dilation rates for preserving the resolution and multi-level aggregation. To incorporate uncertainty, we introduce random transformations during test time for an enhanced segmentation result that simultaneously generates an uncertainty map, highlighting areas of ambiguity. We show that this map can be used to define a metric for disregarding predictions with high uncertainty. The proposed network achieves state-of-the-art performance on the GlaS challenge dataset and on a second independent colorectal adenocarcinoma dataset. In addition, we perform gland instance segmentation on whole-slide images from two further datasets to highlight the generalisability of our method. As an extension, we introduce MILD-Net+ for simultaneous gland and lumen segmentation, to increase the diagnostic power of the network.Comment: Initial version published at Medical Imaging with Deep Learning (MIDL) 201

Deep-Learning for Classification of Colorectal Polyps on Whole-Slide Images

Histopathological characterization of colorectal polyps is an important principle for determining the risk of colorectal cancer and future rates of surveillance for patients. This characterization is time-intensive, requires years of specialized training, and suffers from significant inter-observer and intra-observer variability. In this work, we built an automatic image-understanding method that can accurately classify different types of colorectal polyps in whole-slide histology images to help pathologists with histopathological characterization and diagnosis of colorectal polyps. The proposed image-understanding method is based on deep-learning techniques, which rely on numerous levels of abstraction for data representation and have shown state-of-the-art results for various image analysis tasks. Our image-understanding method covers all five polyp types (hyperplastic polyp, sessile serrated polyp, traditional serrated adenoma, tubular adenoma, and tubulovillous/villous adenoma) that are included in the US multi-society task force guidelines for colorectal cancer risk assessment and surveillance, and encompasses the most common occurrences of colorectal polyps. Our evaluation on 239 independent test samples shows our proposed method can identify the types of colorectal polyps in whole-slide images with a high efficacy (accuracy: 93.0%, precision: 89.7%, recall: 88.3%, F1 score: 88.8%). The presented method in this paper can reduce the cognitive burden on pathologists and improve their accuracy and efficiency in histopathological characterization of colorectal polyps, and in subsequent risk assessment and follow-up recommendations

Few Shot Learning in Histopathological Images:Reducing the Need of Labeled Data on Biological Datasets

Although deep learning pathology diagnostic algorithms are proving comparable results with human experts in a wide variety of tasks, they still require a huge amount of well annotated data for training. Generating such extensive and well labelled datasets is time consuming and is not feasible for certain tasks and so, most of the medical datasets available are scarce in images and therefore, not enough for training. In this work we validate that the use of few shot learning techniques can transfer knowledge from a well defined source domain from Colon tissue into a more generic domain composed by Colon, Lung and Breast tissue by using very few training images. Our results show that our few-shot approach is able to obtain a balanced accuracy (BAC) of 90% with just 60 training images, even for the Lung and Breast tissues that were not present on the training set. This outperforms the finetune transfer learning approach that obtains 73% BAC with 60 images and requires 600 images to get up to 81% BAC.This study has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 732111 (PICCOLO project)

Cascaded Graph Convolution Approach for Nuclei Detection in Histopathology Images

Nuclei detection in histopathology images of can-cerous tissue stained with conventional hematoxylin and eosin stain is a challenging task due to the complexity and diversity of cell data. Deep learning techniques have produced encouraging results in the field of nuclei detection, where the main emphasis is on classification and regression-based methods. Recent research has demonstrated that regression-based techniques outperform classification. In this paper, we propose a classification model based on graph convolutions to classify nuclei, and similar models to detect nuclei using cascaded architecture. With nearly 29,000 annotated nuclei in a large dataset of cancer histology images, we evaluated the Convolutional Neural Network (CNN) and Graph Convolutional Networks (GCN) based approaches. Our findings demonstrate that graph convolutions perform better with a cascaded GCN architecture and are more stable than centre-of-pixel approach. We have compared our two-fold evaluation quantitative results with CNN-based models such as Spatial Constrained Convolutional Neural Network (SC-CNN) and Centre-of-Pixel Convolutional Neural Network (CP-CNN). We used two different loss functions, binary cross-entropy and focal loss function, and also investigated the behaviour of CP-CNN and GCN models to observe the effectiveness of CNN and GCN operators. The compared quantitative F1 score of cascaded-GCN shows an improvement of 6% compared to state-of-the-art methods