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Register a new userDeep Neural Networks Learn Meta-Structures to Segment Fluorescence Microscopy Images
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Added by
Yaoru Luo
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Fluorescence microscopy images play the critical role of capturing spatial or spatiotemporal information of biomedical processes in life sciences. Their simple structures and semantics provide unique advantages in elucidating learning behavior of deep neural networks (DNNs). It is generally assumed that accurate image annotation is required to train DNNs for accurate image segmentation. In this study, however, we find that DNNs trained by label images in which nearly half (49%) of the binary pixel labels are randomly flipped provide largely the same segmentation performance. This suggests that DNNs learn high-level structures rather than pixel-level labels per se to segment fluorescence microscopy images. We refer to these structures as meta-structures. In support of the existence of the meta-structures, when DNNs are trained by a series of label images with progressively less meta-structure information, we find progressive degradation in their segmentation performance. Motivated by the learning behavior of DNNs trained by random labels and the characteristics of meta-structures, we propose an unsupervised segmentation model. Experiments show that it achieves remarkably competitive performance in comparison to supervised segmentation models.
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Microscopy images are powerful tools and widely used in the majority of research areas, such as biology, chemistry, physics and materials fields by various microscopies (scanning electron microscope (SEM), atomic force microscope (AFM) and the optical microscope, et al.). However, most of the microscopy images are colorless due to the unique imaging mechanism. Though investigating on some popular solutions proposed recently about colorizing images, we notice the process of those methods are usually tedious, complicated, and time-consuming. In this paper, inspired by the achievement of machine learning algorithms on different science fields, we introduce two artificial neural networks for gray microscopy image colorization: An end-to-end convolutional neural network (CNN) with a pre-trained model for feature extraction and a pixel-to-pixel neural style transfer convolutional neural network (NST-CNN), which can colorize gray microscopy images with semantic information learned from a user-provided colorful image at inference time. The results demonstrate that our algorithm not only can colorize the microscopy images under complex circumstances precisely but also make the color naturally according to the training of a massive number of nature images with proper hue and saturation.
We propose a novel regularization algorithm to train deep neural networks, in which data at training time is severely biased. Since a neural network efficiently learns data distribution, a network is likely to learn the bias information to categorize input data. It leads to poor performance at test time, if the bias is, in fact, irrelevant to the categorization. In this paper, we formulate a regularization loss based on mutual information between feature embedding and bias. Based on the idea of minimizing this mutual information, we propose an iterative algorithm to unlearn the bias information. We employ an additional network to predict the bias distribution and train the network adversarially against the feature embedding network. At the end of learning, the bias prediction network is not able to predict the bias not because it is poorly trained, but because the feature embedding network successfully unlearns the bias information. We also demonstrate quantitative and qualitative experimental results which show that our algorithm effectively removes the bias information from feature embedding.
Cell instance segmentation in fluorescence microscopy images is becoming essential for cancer dynamics and prognosis. Data extracted from cancer dynamics allows to understand and accurately model different metabolic processes such as proliferation. This enables customized and more precise cancer treatments. However, accurate cell instance segmentation, necessary for further cell tracking and behavior analysis, is still challenging in scenarios with high cell concentration and overlapping edges. Within this framework, we propose a novel cell instance segmentation approach based on the well-known U-Net architecture. To enforce the learning of morphological information per pixel, a deep distance transformer (DDT) acts as a back-bone model. The DDT output is subsequently used to train a top-model. The following top-models are considered: a three-class (emph{e.g.,} foreground, background and cell border) U-net, and a watershed transform. The obtained results suggest a performance boost over traditional U-Net architectures. This opens an interesting research line around the idea of injecting morphological information into a fully convolutional model.
Fluorescence microscopy has enabled a dramatic development in modern biology. Due to its inherently weak signal, fluorescence microscopy is not only much noisier than photography, but also presented with Poisson-Gaussian noise where Poisson noise, or shot noise, is the dominating noise source. To get clean fluorescence microscopy images, it is highly desirable to have effective denoising algorithms and datasets that are specifically designed to denoise fluorescence microscopy images. While such algorithms exist, no such datasets are available. In this paper, we fill this gap by constructing a dataset - the Fluorescence Microscopy Denoising (FMD) dataset - that is dedicated to Poisson-Gaussian denoising. The dataset consists of 12,000 real fluorescence microscopy images obtained with commercial confocal, two-photon, and wide-field microscopes and representative biological samples such as cells, zebrafish, and mouse brain tissues. We use image averaging to effectively obtain ground truth images and 60,000 noisy images with different noise levels. We use this dataset to benchmark 10 representative denoising algorithms and find that deep learning methods have the best performance. To our knowledge, this is the first real microscopy image dataset for Poisson-Gaussian denoising purposes and it could be an important tool for high-quality, real-time denoising applications in biomedical research.
Learning is an inherently continuous phenomenon. When humans learn a new task there is no explicit distinction between training and inference. As we learn a task, we keep learning about it while performing the task. What we learn and how we learn it varies during different stages of learning. Learning how to learn and adapt is a key property that enables us to generalize effortlessly to new settings. This is in contrast with conventional settings in machine learning where a trained model is frozen during inference. In this paper we study the problem of learning to learn at both training and test time in the context of visual navigation. A fundamental challenge in navigation is generalization to unseen scenes. In this paper we propose a self-adaptive visual navigation method (SAVN) which learns to adapt to new environments without any explicit supervision. Our solution is a meta-reinforcement learning approach where an agent learns a self-supervised interaction loss that encourages effective navigation. Our experiments, performed in the AI2-THOR framework, show major improvements in both success rate and SPL for visual navigation in novel scenes. Our code and data are available at: https://github.com/allenai/savn .
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