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Register a new userEnforcing Morphological Information in Fully Convolutional Networks to Improve Cell Instance Segmentation in Fluorescence Microscopy Images
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Added by
Saul Calderon Ramirez
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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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.
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Fluorescence microscopy is an essential tool for the analysis of 3D subcellular structures in tissue. An important step in the characterization of tissue involves nuclei segmentation. In this paper, a two-stage method for segmentation of nuclei using convolutional neural networks (CNNs) is described. In particular, since creating labeled volumes manually for training purposes is not practical due to the size and complexity of the 3D data sets, the paper describes a method for generating synthetic microscopy volumes based on a spatially constrained cycle-consistent adversarial network. The proposed method is tested on multiple real microscopy data sets and outperforms other commonly used segmentation techniques.
In this paper, we present a conceptually simple, strong, and efficient framework for panoptic segmentation, called Panoptic FCN. Our approach aims to represent and predict foreground things and background stuff in a unified fully convolutional pipeline. In particular, Panoptic FCN encodes each object instance or stuff category into a specific kernel weight with the proposed kernel generator and produces the prediction by convolving the high-resolution feature directly. With this approach, instance-aware and semantically consistent properties for things and stuff can be respectively satisfied in a simple generate-kernel-then-segment workflow. Without extra boxes for localization or instance separation, the proposed approach outperforms previous box-based and -free models with high efficiency on COCO, Cityscapes, and Mapillary Vistas datasets with single scale input. Our code is made publicly available at https://github.com/Jia-Research-Lab/PanopticFCN.
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.
Due to the worlds demand for security systems, biometrics can be seen as an important topic of research in computer vision. One of the biometric forms that has been gaining attention is the recognition based on sclera. The initial and paramount step for performing this type of recognition is the segmentation of the region of interest, i.e. the sclera. In this context, two approaches for such task based on the Fully Convolutional Network (FCN) and on Generative Adversarial Network (GAN) are introduced in this work. FCN is similar to a common convolution neural network, however the fully connected layers (i.e., the classification layers) are removed from the end of the network and the output is generated by combining the output of pooling layers from different convolutional ones. The GAN is based on the game theory, where we have two networks competing with each other to generate the best segmentation. In order to perform fair comparison with baselines and quantitative and objective evaluations of the proposed approaches, we provide to the scientific community new 1,300 manually segmented images from two databases. The experiments are performed on the UBIRIS.v2 and MICHE databases and the best performing configurations of our propositions achieved F-scores measures of 87.48% and 88.32%, respectively.
We desgin a novel fully convolutional network architecture for shapes, denoted by Shape Fully Convolutional Networks (SFCN). 3D shapes are represented as graph structures in the SFCN architecture, based on novel graph convolution and pooling operations, which are similar to convolution and pooling operations used on images. Meanwhile, to build our SFCN architecture in the original image segmentation fully convolutional network (FCN) architecture, we also design and implement a generating operation} with bridging function. This ensures that the convolution and pooling operation we have designed can be successfully applied in the original FCN architecture. In this paper, we also present a new shape segmentation approach based on SFCN. Furthermore, we allow more general and challenging input, such as mixed datasets of different categories of shapes} which can prove the ability of our generalisation. In our approach, SFCNs are trained triangles-to-triangles by using three low-level geometric features as input. Finally, the feature voting-based multi-label graph cuts is adopted to optimise the segmentation results obtained by SFCN prediction. The experiment results show that our method can effectively learn and predict mixed shape datasets of either similar or different characteristics, and achieve excellent segmentation results.
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