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Register a new userSemantic Segmentation of highly class imbalanced fully labelled 3D volumetric biomedical images and unsupervised Domain Adaptation of the pre-trained Segmentation Network to segment another fully unlabelled Biomedical 3D Image stack
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Shreya Roy
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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The goal of our work is to perform pixel label semantic segmentation on 3D biomedical volumetric data. Manual annotation is always difficult for a large bio-medical dataset. So, we consider two cases where one dataset is fully labeled and the other dataset is assumed to be fully unlabelled. We first perform Semantic Segmentation on the fully labeled isotropic biomedical source data (FIBSEM) and try to incorporate the the trained model for segmenting the target unlabelled dataset(SNEMI3D)which shares some similarities with the source dataset in the context of different types of cellular bodies and other cellular components. Although, the cellular components vary in size and shape. So in this paper, we have proposed a novel approach in the context of unsupervised domain adaptation while classifying each pixel of the target volumetric data into cell boundary and cell body. Also, we have proposed a novel approach to giving non-uniform weights to different pixels in the training images while performing the pixel-level semantic segmentation in the presence of the corresponding pixel-wise label map along with the training original images in the source domain. We have used the Entropy Map or a Distance Transform matrix retrieved from the given ground truth label map which has helped to overcome the class imbalance problem in the medical image data where the cell boundaries are extremely thin and hence, extremely prone to be misclassified as non-boundary.
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Segmentation of 3D images is a fundamental problem in biomedical image analysis. Deep learning (DL) approaches have achieved state-of-the-art segmentation perfor- mance. To exploit the 3D contexts using neural networks, known DL segmentation methods, including 3D convolution, 2D convolution on planes orthogonal to 2D image slices, and LSTM in multiple directions, all suffer incompatibility with the highly anisotropic dimensions in common 3D biomedical images. In this paper, we propose a new DL framework for 3D image segmentation, based on a com- bination of a fully convolutional network (FCN) and a recurrent neural network (RNN), which are responsible for exploiting the intra-slice and inter-slice contexts, respectively. To our best knowledge, this is the first DL framework for 3D image segmentation that explicitly leverages 3D image anisotropism. Evaluating using a dataset from the ISBI Neuronal Structure Segmentation Challenge and in-house image stacks for 3D fungus segmentation, our approach achieves promising results comparing to the known DL-based 3D segmentation approaches.
With pervasive applications of medical imaging in health-care, biomedical image segmentation plays a central role in quantitative analysis, clinical diagno- sis, and medical intervention. Since manual anno- tation su ers limited reproducibility, arduous e orts, and excessive time, automatic segmentation is desired to process increasingly larger scale histopathological data. Recently, deep neural networks (DNNs), par- ticularly fully convolutional networks (FCNs), have been widely applied to biomedical image segmenta- tion, attaining much improved performance. At the same time, quantization of DNNs has become an ac- tive research topic, which aims to represent weights with less memory (precision) to considerably reduce memory and computation requirements of DNNs while maintaining acceptable accuracy. In this paper, we apply quantization techniques to FCNs for accurate biomedical image segmentation. Unlike existing litera- ture on quantization which primarily targets memory and computation complexity reduction, we apply quan- tization as a method to reduce over tting in FCNs for better accuracy. Speci cally, we focus on a state-of- the-art segmentation framework, suggestive annotation [22], which judiciously extracts representative annota- tion samples from the original training dataset, obtain- ing an e ective small-sized balanced training dataset. We develop two new quantization processes for this framework: (1) suggestive annotation with quantiza- tion for highly representative training samples, and (2) network training with quantization for high accuracy. Extensive experiments on the MICCAI Gland dataset show that both quantization processes can improve the segmentation performance, and our proposed method exceeds the current state-of-the-art performance by up to 1%. In addition, our method has a reduction of up to 6.4x on memory usage.
Unsupervised Domain Adaptation (UDA) is crucial to tackle the lack of annotations in a new domain. There are many multi-modal datasets, but most UDA approaches are uni-modal. In this work, we explore how to learn from multi-modality and propose cross-modal UDA (xMUDA) where we assume the presence of 2D images and 3D point clouds for 3D semantic segmentation. This is challenging as the two input spaces are heterogeneous and can be impacted differently by domain shift. In xMUDA, modalities learn from each other through mutual mimicking, disentangled from the segmentation objective, to prevent the stronger modality from adopting false predictions from the weaker one. We evaluate on new UDA scenarios including day-to-night, country-to-country and dataset-to-dataset, leveraging recent autonomous driving datasets. xMUDA brings large improvements over uni-modal UDA on all tested scenarios, and is complementary to state-of-the-art UDA techniques. Code is available at https://github.com/valeoai/xmuda.
3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own strengths and weaknesses, and by unifying them together, one may be able to achieve more accurate results. In this paper, we propose a new ensemble learning framework for 3D biomedical image segmentation that combines the merits of 2D and 3D models. First, we develop a fully convolutional network based meta-learner to learn how to improve the results from 2D and 3D models (base-learners). Then, to minimize over-fitting for our sophisticated meta-learner, we devise a new training method that uses the results of the base-learners as multip
Semantic segmentation is essentially important to biomedical image analysis. Many recent works mainly focus on integrating the Fully Convolutional Network (FCN) architecture with sophisticated convolution implementation and deep supervision. In this paper, we propose to decompose the single segmentation task into three subsequent sub-tasks, including (1) pixel-wise image segmentation, (2) prediction of the class labels of the objects within the image, and (3) classification of the scene the image belonging to. While these three sub-tasks are trained to optimize their individual loss functions of different perceptual levels, we propose to let them interact by the task-task context ensemble. Moreover, we propose a novel sync-regularization to penalize the deviation between the outputs of the pixel-wise segmentation and the class prediction tasks. These effective regularizations help FCN utilize context information comprehensively and attain accurate semantic segmentation, even though the number of the images for training may be limited in many biomedical applications. We have successfully applied our framework to three diverse 2D/3D medical image datasets, including Robotic Scene Segmentation Challenge 18 (ROBOT18), Brain Tumor Segmentation Challenge 18 (BRATS18), and Retinal Fundus Glaucoma Challenge (REFUGE18). We have achieved top-tier performance in all three challenges.
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