scholarly journals An Empirical Evaluation of Nuclei Segmentation from H&E Images in a Real Application Scenario

2020 ◽  
Vol 10 (22) ◽  
pp. 7982
Author(s):  
Lorenzo Putzu ◽  
Giorgio Fumera
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Real World ◽  
Domain Adaptation ◽  
State Of The Art ◽  
Empirical Evaluation ◽  
Training Data ◽  
Cell Nuclei ◽  
Nuclei Segmentation ◽  
Segmentation Methods

Cell nuclei segmentation is a challenging task, especially in real applications, when the target images significantly differ between them. This task is also challenging for methods based on convolutional neural networks (CNNs), which have recently boosted the performance of cell nuclei segmentation systems. However, when training data are scarce or not representative of deployment scenarios, they may suffer from overfitting to a different extent, and may hardly generalise to images that differ from the ones used for training. In this work, we focus on real-world, challenging application scenarios when no annotated images from a given dataset are available, or when few images (even unlabelled) of the same domain are available to perform domain adaptation. To simulate this scenario, we performed extensive cross-dataset experiments on several CNN-based state-of-the-art cell nuclei segmentation methods. Our results show that some of the existing CNN-based approaches are capable of generalising to target images which resemble the ones used for training. In contrast, their effectiveness considerably degrades when target and source significantly differ in colours and scale.

scholarly journals ADVERSARIAL DOMAIN ADAPTATION FOR THE CLASSIFICATION OF AERIAL IMAGES AND HEIGHT DATA USING CONVOLUTIONAL NEURAL NETWORKS

2019 ◽  
Vol IV-2/W7 ◽  
pp. 197-204 ◽  
Author(s):  
D. Wittich ◽  
F. Rottensteiner
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Domain Adaptation ◽  
Feature Representation ◽  
Training Data ◽  
Aerial Images ◽  
Remotely Sensed Data ◽  
Target Domain ◽  
Deep Convolutional Neural Networks

<p><strong>Abstract.</strong> Domain adaptation (DA) can drastically decrease the amount of training data needed to obtain good classification models by leveraging available data from a source domain for the classification of a new (target) domains. In this paper, we address deep DA, i.e. DA with deep convolutional neural networks (CNN), a problem that has not been addressed frequently in remote sensing. We present a new method for semi-supervised DA for the task of pixel-based classification by a CNN. After proposing an encoder-decoder-based fully convolutional neural network (FCN), we adapt a method for adversarial discriminative DA to be applicable to the pixel-based classification of remotely sensed data based on this network. It tries to learn a feature representation that is domain invariant; domain-invariance is measured by a classifier’s incapability of predicting from which domain a sample was generated. We evaluate our FCN on the ISPRS labelling challenge, showing that it is close to the best-performing models. DA is evaluated on the basis of three domains. We compare different network configurations and perform the representation transfer at different layers of the network. We show that when using a proper layer for adaptation, our method achieves a positive transfer and thus an improved classification accuracy in the target domain for all evaluated combinations of source and target domains.</p>

scholarly journals A review and comparison of breast tumor cell nuclei segmentation performances using deep convolutional neural networks

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Andrew Lagree ◽  
Majidreza Mohebpour ◽  
Nicholas Meti ◽  
Khadijeh Saednia ◽  
Fang-I. Lu ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Breast Tissue ◽  
Superior Performance ◽  
Histopathological Analysis ◽  
Cell Nuclei ◽  
Deep Convolutional Neural Networks ◽  
Nuclei Segmentation ◽  
Histopathological Images ◽  
Biopsy Examination

AbstractBreast cancer is currently the second most common cause of cancer-related death in women. Presently, the clinical benchmark in cancer diagnosis is tissue biopsy examination. However, the manual process of histopathological analysis is laborious, time-consuming, and limited by the quality of the specimen and the experience of the pathologist. This study's objective was to determine if deep convolutional neural networks can be trained, with transfer learning, on a set of histopathological images independent of breast tissue to segment tumor nuclei of the breast. Various deep convolutional neural networks were evaluated for the study, including U-Net, Mask R-CNN, and a novel network (GB U-Net). The networks were trained on a set of Hematoxylin and Eosin (H&E)-stained images of eight diverse types of tissues. GB U-Net demonstrated superior performance in segmenting sites of invasive diseases (AJI = 0.53, mAP = 0.39 & AJI = 0.54, mAP = 0.38), validated on two hold-out datasets exclusively containing breast tissue images of approximately 7,582 annotated cells. The results of the networks, trained on images independent of breast tissue, demonstrated that tumor nuclei of the breast could be accurately segmented.

scholarly journals Automatic image annotation for fluorescent cell nuclei segmentation

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250093
Author(s):  
Fabian Englbrecht ◽  
Iris E. Ruider ◽  
Andreas R. Bausch
Keyword(s):  
Neural Networks ◽  
Data Augmentation ◽  
Image Annotation ◽  
Image Data ◽  
Training Data ◽  
Third Party ◽  
Cell Nuclei ◽  
Fluorescent Cell ◽  
Data Annotation ◽  
Nuclei Segmentation

Dataset annotation is a time and labor-intensive task and an integral requirement for training and testing deep learning models. The segmentation of images in life science microscopy requires annotated image datasets for object detection tasks such as instance segmentation. Although the amount of annotated image data has been steadily reduced due to methods such as data augmentation, the process of manual or semi-automated data annotation is the most labor and cost intensive task in the process of cell nuclei segmentation with deep neural networks. In this work we propose a system to fully automate the annotation process of a custom fluorescent cell nuclei image dataset. By that we are able to reduce nuclei labelling time by up to 99.5%. The output of our system provides high quality training data for machine learning applications to identify the position of cell nuclei in microscopy images. Our experiments have shown that the automatically annotated dataset provides coequal segmentation performance compared to manual data annotation. In addition, we show that our system enables a single workflow from raw data input to desired nuclei segmentation and tracking results without relying on pre-trained models or third-party training datasets for neural networks.

scholarly journals Graph Convolutional Networks for Text Classification

2019 ◽  
Vol 33 ◽  
pp. 7370-7377 ◽  
Author(s):  
Liang Yao ◽  
Chengsheng Mao ◽  
Yuan Luo
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Language Processing ◽  
Text Classification ◽  
State Of The Art ◽  
Classical Problem ◽  
Experimental Results ◽  
Training Data ◽  
Convolutional Networks ◽  
Single Text

Text classification is an important and classical problem in natural language processing. There have been a number of studies that applied convolutional neural networks (convolution on regular grid, e.g., sequence) to classification. However, only a limited number of studies have explored the more flexible graph convolutional neural networks (convolution on non-grid, e.g., arbitrary graph) for the task. In this work, we propose to use graph convolutional networks for text classification. We build a single text graph for a corpus based on word co-occurrence and document word relations, then learn a Text Graph Convolutional Network (Text GCN) for the corpus. Our Text GCN is initialized with one-hot representation for word and document, it then jointly learns the embeddings for both words and documents, as supervised by the known class labels for documents. Our experimental results on multiple benchmark datasets demonstrate that a vanilla Text GCN without any external word embeddings or knowledge outperforms state-of-the-art methods for text classification. On the other hand, Text GCN also learns predictive word and document embeddings. In addition, experimental results show that the improvement of Text GCN over state-of-the-art comparison methods become more prominent as we lower the percentage of training data, suggesting the robustness of Text GCN to less training data in text classification.

scholarly journals What is this Article about? Extreme Summarization with Topic-aware Convolutional Neural Networks

2019 ◽  
Vol 66 ◽  
pp. 243-278
Author(s):  
Shashi Narayan ◽  
Shay B. Cohen ◽  
Mirella Lapata
Keyword(s):  
Neural Networks ◽  
Long Range ◽  
Convolutional Neural Networks ◽  
Real World ◽  
Large Scale ◽  
State Of The Art ◽  
British Broadcasting Corporation ◽  
Document Summarization ◽  
Modeling Approach ◽  
Large Scale Dataset

We introduce "extreme summarization," a new single-document summarization task which aims at creating a short, one-sentence news summary answering the question "What is the article about?". We argue that extreme summarization, by nature, is not amenable to extractive strategies and requires an abstractive modeling approach. In the hope of driving research on this task further: (a) we collect a real-world, large scale dataset by harvesting online articles from the British Broadcasting Corporation (BBC); and (b) propose a novel abstractive model which is conditioned on the article's topics and based entirely on convolutional neural networks. We demonstrate experimentally that this architecture captures long-range dependencies in a document and recognizes pertinent content, outperforming an oracle extractive system and state-of-the-art abstractive approaches when evaluated automatically and by humans on the extreme summarization dataset.

scholarly journals An automatic nuclei segmentation method based on deep convolutional neural networks for histopathology images

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Hwejin Jung ◽  
Bilal Lodhi ◽  
Jaewoo Kang
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Gaussian Mixture ◽  
Color Variation ◽  
Post Processing ◽  
Segmentation Method ◽  
Deep Convolutional Neural Networks ◽  
Nuclei Segmentation ◽  
Histopathology Images

Abstract Background Since nuclei segmentation in histopathology images can provide key information for identifying the presence or stage of a disease, the images need to be assessed carefully. However, color variation in histopathology images, and various structures of nuclei are two major obstacles in accurately segmenting and analyzing histopathology images. Several machine learning methods heavily rely on hand-crafted features which have limitations due to manual thresholding. Results To obtain robust results, deep learning based methods have been proposed. Deep convolutional neural networks (DCNN) used for automatically extracting features from raw image data have been proven to achieve great performance. Inspired by such achievements, we propose a nuclei segmentation method based on DCNNs. To normalize the color of histopathology images, we use a deep convolutional Gaussian mixture color normalization model which is able to cluster pixels while considering the structures of nuclei. To segment nuclei, we use Mask R-CNN which achieves state-of-the-art object segmentation performance in the field of computer vision. In addition, we perform multiple inference as a post-processing step to boost segmentation performance. We evaluate our segmentation method on two different datasets. The first dataset consists of histopathology images of various organ while the other consists histopathology images of the same organ. Performance of our segmentation method is measured in various experimental setups at the object-level and the pixel-level. In addition, we compare the performance of our method with that of existing state-of-the-art methods. The experimental results show that our nuclei segmentation method outperforms the existing methods. Conclusions We propose a nuclei segmentation method based on DCNNs for histopathology images. The proposed method which uses Mask R-CNN with color normalization and multiple inference post-processing provides robust nuclei segmentation results. Our method also can facilitate downstream nuclei morphological analyses as it provides high-quality features extracted from histopathology images.

scholarly journals Soft Filter Pruning for Accelerating Deep Convolutional Neural Networks

2018 ◽  
Author(s):  
Yang He ◽  
Guoliang Kang ◽  
Xuanyi Dong ◽  
Yanwei Fu ◽  
Yi Yang
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
The State ◽  
Training Data ◽  
Deep Convolutional Neural Networks ◽  
Inference Procedure ◽  
Accuracy Improvement ◽  
Large Capacity ◽  
Pruning Methods

This paper proposed a Soft Filter Pruning (SFP) method to accelerate the inference procedure of deep Convolutional Neural Networks (CNNs). Specifically, the proposed SFP enables the pruned filters to be updated when training the model after pruning. SFP has two advantages over previous works: (1) Larger model capacity. Updating previously pruned filters provides our approach with larger optimization space than fixing the filters to zero. Therefore, the network trained by our method has a larger model capacity to learn from the training data. (2) Less dependence on the pretrained model. Large capacity enables SFP to train from scratch and prune the model simultaneously. In contrast, previous filter pruning methods should be conducted on the basis of the pre-trained model to guarantee their performance. Empirically, SFP from scratch outperforms the previous filter pruning methods. Moreover, our approach has been demonstrated effective for many advanced CNN architectures. Notably, on ILSCRC-2012, SFP reduces more than 42% FLOPs on ResNet-101 with even 0.2% top-5 accuracy improvement, which has advanced the state-of-the-art. Code is publicly available on GitHub: https://github.com/he-y/softfilter-pruning

scholarly journals Using spatial-temporal ensembles of convolutional neural networks for lumen segmentation in ureteroscopy

2021 ◽  
Author(s):  
Jorge F. Lazo ◽  
Aldo Marzullo ◽  
Sara Moccia ◽  
Michele Catellani ◽  
Benoit Rosa ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Automatic Segmentation ◽  
Temporal Information ◽  
Invasive Technique ◽  
Dice Similarity Coefficient ◽  
Specular Reflections ◽  
Lumen Segmentation ◽  
Previous State

Abstract Purpose Ureteroscopy is an efficient endoscopic minimally invasive technique for the diagnosis and treatment of upper tract urothelial carcinoma. During ureteroscopy, the automatic segmentation of the hollow lumen is of primary importance, since it indicates the path that the endoscope should follow. In order to obtain an accurate segmentation of the hollow lumen, this paper presents an automatic method based on convolutional neural networks (CNNs). Methods The proposed method is based on an ensemble of 4 parallel CNNs to simultaneously process single and multi-frame information. Of these, two architectures are taken as core-models, namely U-Net based in residual blocks ($$m_1$$ m 1 ) and Mask-RCNN ($$m_2$$ m 2 ), which are fed with single still-frames I(t). The other two models ($$M_1$$ M 1 , $$M_2$$ M 2 ) are modifications of the former ones consisting on the addition of a stage which makes use of 3D convolutions to process temporal information. $$M_1$$ M 1 , $$M_2$$ M 2 are fed with triplets of frames ($$I(t-1)$$ I ( t - 1 ) , I(t), $$I(t+1)$$ I ( t + 1 ) ) to produce the segmentation for I(t). Results The proposed method was evaluated using a custom dataset of 11 videos (2673 frames) which were collected and manually annotated from 6 patients. We obtain a Dice similarity coefficient of 0.80, outperforming previous state-of-the-art methods. Conclusion The obtained results show that spatial-temporal information can be effectively exploited by the ensemble model to improve hollow lumen segmentation in ureteroscopic images. The method is effective also in the presence of poor visibility, occasional bleeding, or specular reflections.

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