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1. SRNet: Spatial Relation Network for Efficient Single Stage Instance Segmentation in Videos

   Ying, Xiaowen ; Li, Xin ; Chuah, Mooi Choo ( October 2021 , ACM Multimedia 2021)

   The task of instance segmentation in videos aims to consistently identify objects at pixel level throughout the entire video sequence. Existing state-of-the-art methods either follow the tracking-bydetection paradigm to employ multi-stage pipelines or directly train a complex deep model to process the entire video clips as 3D volumes. However, these methods are typically slow and resourceconsuming such that they are often limited to offline processing. In this paper, we propose SRNet, a simple and efficient framework for joint segmentation and tracking of object instances in videos. The key to achieving both high efficiency and accuracy in our framework is to formulate the instance segmentation and tracking problem into a unified spatial-relation learning task where each pixel in the current frame relates to its object center, and each object center relates to its location in the previous frame. This unified learning framework allows our framework to perform join instance segmentation and tracking through a single stage while maintaining low overheads among different learning tasks. Our proposed framework can handle two different task settings and demonstrates comparable performance with state-of-the-art methods on two different benchmarks while running significantly faster.
2. PIXEL-WISE NEURAL CELL INSTANCE SEGMENTATION

   Yi, J. ; Wu, P. ; Hoeppner, D. J. ; Metaxas, D. ( April 2018 , 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018))

   Accurate cell instance segmentation plays an important role in the study of neural cell interactions, which are critical for understanding the development of brain. These interactions are performed through the filopodia and lamellipodia of neural cells, which are extremely tiny structures and as a result render most existing instance segmentation methods powerless to precisely capture them. To solve this issue, in this paper we present a novel hierarchical neural network comprising object detection and segmentation modules. Compared to previous work, our model is able to efficiently share and make full use of the information at different levels between the two modules. Our method is simple yet powerful, and experimental results show that it captures the contours of neural cells, especially the filopodia and lamellipodia, with high accuracy, and outperforms recent state of the art by a large margin.
3. AxonEM Dataset: 3D Axon Instance Segmentation of Brain Cortical Regions

   https://doi.org/10.1007/978-3-030-87193-2_17  

   Wei, D ; Lee, K ; Li, H ; Lu, H ; Bae, J ; Liu, Z ; Zhang, L ; dos Santos, M ; Lin, Z ; Uram, T ; et al ( January 2021 , International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI))

   Electron microscopy (EM) enables the reconstruction of neural circuits at the level of individual synapses, which has been transformative for scientific discoveries. However, due to the complex morphology, an accurate reconstruction of cortical axons has become a major challenge. Worse still, there is no publicly available large-scale EM dataset from the cortex that provides dense ground truth segmentation for axons, making it difficult to develop and evaluate large-scale axon reconstruction methods. To address this, we introduce the AxonEM dataset, which consists of two 30x30x30 cubic mm EM image volumes from the human and mouse cortex, respectively. We thoroughly proofread over 18,000 axon instances to provide dense 3D axon instance segmentation, enabling large- scale evaluation of axon reconstruction methods. In addition, we densely annotate nine ground truth subvolumes for training, per each data volume. With this, we reproduce two published state-of-the-art methods and provide their evaluation results as a baseline. We publicly release our code and data at https://connectomics-bazaar.github.io/proj/ AxonEM/index.html to foster the development of advanced methods.
4. DeepIsoFun: a deep domain adaptation approach to predict isoform functions

   https://doi.org/10.1093/bioinformatics/bty1017  

   Shaw, Dipan ; Chen, Hao ; Jiang, Tao ; Hancock, John ( December 2018 , Bioinformatics)

   Abstract Motivation Isoforms are mRNAs produced from the same gene locus by alternative splicing and may have different functions. Although gene functions have been studied extensively, little is known about the specific functions of isoforms. Recently, some computational approaches based on multiple instance learning have been proposed to predict isoform functions from annotated gene functions and expression data, but their performance is far from being desirable primarily due to the lack of labeled training data. To improve the performance on this problem, we propose a novel deep learning method, DeepIsoFun, that combines multiple instance learning with domain adaptation. The latter technique helps to transfer the knowledge of gene functions to the prediction of isoform functions and provides additional labeled training data. Our model is trained on a deep neural network architecture so that it can adapt to different expression distributions associated with different gene ontology terms. Results We evaluated the performance of DeepIsoFun on three expression datasets of human and mouse collected from SRA studies at different times. On each dataset, DeepIsoFun performed significantly better than the existing methods. In terms of area under the receiver operating characteristics curve, our method acquired at least 26% improvement and in terms ofmore »area under the precision-recall curve, it acquired at least 10% improvement over the state-of-the-art methods. In addition, we also study the divergence of the functions predicted by our method for isoforms from the same gene and the overall correlation between expression similarity and the similarity of predicted functions. Availability and implementation https://github.com/dls03/DeepIsoFun/ Supplementary information Supplementary data are available at Bioinformatics online.« less
5. Deep Variational Instance Segmentation

   Yuan, Jialin ; Chen, Chao ; Li, Fuxin ( October 2020 , Advances in neural information processing systems)

   Instance segmentation, which seeks to obtain both class and instance labels for each pixel in the input image, is a challenging task in computer vision. State-ofthe-art algorithms often employ a search-based strategy, which first divides the output image with a regular grid and generate proposals at each grid cell, then the proposals are classified and boundaries refined. In this paper, we propose a novel algorithm that directly utilizes a fully convolutional network (FCN) to predict instance labels. Specifically, we propose a variational relaxation of instance segmentation as minimizing an optimization functional for a piecewise-constant segmentation problem, which can be used to train an FCN end-to-end. It extends the classical Mumford-Shah variational segmentation algorithm to be able to handle the permutation-invariant ground truth in instance segmentation. Experiments on PASCAL VOC 2012 and the MSCOCO 2017 dataset show that the proposed approach efficiently tackles the instance segmentation task. The source code and trained models are released at https://github.com/jia2lin3yuan1/2020-instanceSeg.