BIOMEDICAL SEGMENTATION ON CELL AND BRAIN IMAGES

The biomedical imaging techniques grow rapidly and output big amount of data quickly in the recent years. But image segmentation, one of the most important and fundamental biomedical data analysis techniques, is still time-consuming for human annotators. Therefore, there is an urgent need for segmentation to be taken by machine automatically. Segmentation is essential for biomedical image analysis and could help researchers to gain further diagnostic insights. This paper has three topics under biomedical image segmentation scenario. For the first topic, we examine a popular deep learning structure for segmentation task, U-Net, and modify it for our task on bacteria cell images by using boundary label setting and weighted loss function. Compared to the MATLAB segmentation program used before, the new deep learning method improves the performance in terms of object-level evaluation metrics. For the second topic, we participate into a brain image segmentation challenge which aims for helping neuroscientists to segment the membrane from neurites in order to get the reconstruction of neurites circuit. Data augmentation tricks and multiple loss functions are examined for improving the test performance and finally using combined loss functions can out-perform the original U-Net result in terms of the official ranking metric. A new dice loss is designed to focus more on the hard to segment class. The third topic is to apply the unsupervised segmentation method which will not be restrained by human labelling speed and effort. This is meaningful under biomedical segmentation scenario where training data with expert labelling is always lacking. Without using any labelled data, the unsupervised method, Double DIP, performs better than the MATLAB program on the semantic level

Review : Deep learning in electron microscopy

Deep learning is transforming most areas of science and technology, including electron microscopy. This review paper offers a practical perspective aimed at developers with limited familiarity. For context, we review popular applications of deep learning in electron microscopy. Following, we discuss hardware and software needed to get started with deep learning and interface with electron microscopes. We then review neural network components, popular architectures, and their optimization. Finally, we discuss future directions of deep learning in electron microscopy

Advancing efficiency and robustness of neural networks for imaging

Enabling machines to see and analyze the world is a longstanding research objective. Advances in computer vision have the potential of influencing many aspects of our lives as they can enable machines to tackle a variety of tasks. Great progress in computer vision has been made, catalyzed by recent progress in machine learning and especially the breakthroughs achieved by deep artificial neural networks. Goal of this work is to alleviate limitations of deep neural networks that hinder their large-scale adoption for real-world applications. To this end, it investigates methodologies for constructing and training deep neural networks with low computational requirements. Moreover, it explores strategies for achieving robust performance on unseen data. Of particular interest is the application of segmenting volumetric medical scans because of the technical challenges it imposes, as well as its clinical importance. The developed methodologies are generic and of relevance to a broader computer vision and machine learning audience. More specifically, this work introduces an efficient 3D convolutional neural network architecture, which achieves high performance for segmentation of volumetric medical images, an application previously hindered by high computational requirements of 3D networks. It then investigates sensitivity of network performance on hyper-parameter configuration, which we interpret as overfitting the model configuration to the data available during development. It is shown that ensembling a set of models with diverse configurations mitigates this and improves generalization. The thesis then explores how to utilize unlabelled data for learning representations that generalize better. It investigates domain adaptation and introduces an architecture for adversarial networks tailored for adaptation of segmentation networks. Finally, a novel semi-supervised learning method is proposed that introduces a graph in the latent space of a neural network to capture relations between labelled and unlabelled samples. It then regularizes the embedding to form a compact cluster per class, which improves generalization.Open Acces

Adaptive Fusion Techniques for Effective Multimodal Deep Learning

Effective fusion of data from multiple modalities, such as video, speech, and text, is a challenging task due to the heterogeneous nature of multimodal data. In this work, we propose fusion techniques that aim to model context from different modalities effectively. Instead of defining a deterministic fusion operation, such as concatenation, for the network, we let the network decide “how” to combine given multimodal features more effectively. We propose two networks: 1) Auto-Fusion network, which aims to compress information from different modalities while preserving the context, and 2) GAN-Fusion, which regularizes the learned latent space given context from complementing modalities. A quantitative evaluation on the tasks of multimodal machine translation and emotion recognition suggests that our adaptive networks can better model context from other modalities than all existing methods, many of which employ massive transformer-based networks

On Improving Generalization of CNN-Based Image Classification with Delineation Maps Using the CORF Push-Pull Inhibition Operator

Deployed image classification pipelines are typically dependent on the images captured in real-world environments. This means that images might be affected by different sources of perturbations (e.g. sensor noise in low-light environments). The main challenge arises by the fact that image quality directly impacts the reliability and consistency of classification tasks. This challenge has, hence, attracted wide interest within the computer vision communities. We propose a transformation step that attempts to enhance the generalization ability of CNN models in the presence of unseen noise in the test set. Concretely, the delineation maps of given images are determined using the CORF push-pull inhibition operator. Such an operation transforms an input image into a space that is more robust to noise before being processed by a CNN. We evaluated our approach on the Fashion MNIST data set with an AlexNet model. It turned out that the proposed CORF-augmented pipeline achieved comparable results on noise-free images to those of a conventional AlexNet classification model without CORF delineation maps, but it consistently achieved significantly superior performance on test images perturbed with different levels of Gaussian and uniform noise