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1. Local Shape Descriptors for Neuron Segmentation

   https://doi.org/10.1101/2021.01.18.427039  

   Sheridan, Arlo; Nguyen, Tri; Deb, Diptodip; Lee, Wei-Chung Allen; Saalfeld, Stephan; Turaga, Srini; Manor, Uri; Funke, Jan (January 2021, bioRxiv)

   null (Ed.)

   We present a simple, yet effective, auxiliary learning task for the problem of neuron segmentation in electron microscopy volumes. The auxiliary task consists of the prediction of Local Shape Descriptors (LSDs), which we combine with conventional voxel-wise direct neighbor affinities for neuron boundary detection. The shape descriptors are designed to capture local statistics about the neuron to be segmented, such as diameter, elongation, and direction.On a large study comparing several existing methods across various specimen, imaging techniques, and resolutions, we find that auxiliary learning of LSDs consistently increases segmentation accuracy of affinity-based methods over a range of metrics. Furthermore, the addition of LSDs promotes affinity-based segmentation methods to be on par with the current state of the art for neuron segmentation (Flood-Filling Networks,FFN), while being two orders of magnitudes more efficient—a critical requirement for the processing of future petabyte-sized datasets. Implementations of the new auxiliary learning task,network architectures, training, prediction, and evaluation code, as well as the datasets used in this study are publicly available as a benchmark for future method contributions. 

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2. Biologically-Constrained Graphs for Global Connectomics Reconstruction

   Matejek, Brian; Haehn, Daniel; Zhu, Haidong; Wei, Donglai; Parag, Toufiq; Pfister, Hanspeter (January 2019, IEEE Computer Society Conference on Computer Vision and Pattern Recognition)

   Most current state-of-the-art connectome reconstruction pipelines have two major steps: initial pixel-based segmentation with affinity prediction and watershed transform, and refined segmentation by merging over-segmented regions. These methods rely only on local context and are typically agnostic to the underlying biology. Since a few merge errors can lead to several incorrectly merged neuronal processes, these algorithms are currently tuned towards over-segmentation producing an overburden of costly proofreading. We propose a third step for connectomics reconstruction pipelines to refine an over-segmentation using both local and global context with an emphasis on adhering to the underlying biology. We first extract a graph from an input segmentation where nodes correspond to segment labels and edges indicate potential split errors in the over-segmentation. In order to increase throughput and allow for large-scale reconstruction, we employ biologically inspired geometric constraints based on neuron morphology to reduce the number of nodes and edges. Next, two neural networks learn these neuronal shapes to further aid the graph construction process. Lastly, we reformulate the region merging problem as a graph partitioning one to leverage global context. We demonstrate the performance of our approach on four real-world connectomics datasets with an average variation of information improvement of 21.3%. 

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3. Simultaneous Multi-Level Descriptor Learning and Semantic Segmentation for Domain-Specific Relocalization

   https://doi.org/10.1109/ICRA48506.2021.9561964  

   Wu, Xiaolong; Chen, Yiye; Pradalier, Cedric; Vela, Patricio A. (May 2021, International Conference on Robotics and Automation)

   This paper presents a semi-supervised framework for multi-level description learning aiming for robust and accurate camera relocalization across large perception variations. Our proposed network, namely DLSSNet, simultaneously learns weakly-supervised semantic segmentation and local feature description in the hierarchy. Therefore, the augmented descriptors, trained in an end-to-end manner, provide a more stable high-level representation for local feature dis-ambiguity. To facilitate end-to-end semantic description learning, the descriptor segmentation module is proposed to jointly learn semantic descriptors and cluster centers using standard semantic segmentation loss. We show that our model can be easily fine-tuned for domain-specific usage without any further semantic annotations, instead, requiring only 2D-2D pixel correspondences. The learned descriptors, trained with our proposed pipeline, can boost the cross-season localization performance against other state-of-the-arts. 

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4. Directionally Convolutional Networks for 3D Shape Segmentation

   Xu, Haotian; Dong, Ming; Zhong, Zichun (January 2017, IEEE International Conference on Computer Vision (ICCV))

   Previous approaches on 3D shape segmentation mostly rely on heuristic processing and hand-tuned geometric descriptors. In this paper, we propose a novel 3D shape representation learning approach, Directionally Convolutional Network (DCN), to solve the shape segmentation problem. DCN extends convolution operations from images to the surface mesh of 3D shapes. With DCN, we learn effective shape representations from raw geometric features, i.e., face normals and distances, to achieve robust segmentation. More specifically, a two-stream segmentation framework is proposed: one stream is made up by the proposed DCN with the face normals as the input, and the other stream is implemented by a neural network with the face distance histogram as the input. The learned shape representations from the two streams are fused by an element-wise product. Finally, Conditional Random Field (CRF) is applied to optimize the segmentation. Through extensive experiments conducted on benchmark datasets, we demonstrate that our approach outperforms the current state-of-the-arts (both classic and deep learning-based) on a large variety of 3D shapes. 

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5. MIMO U-Net: efficient cell segmentation and counting in microscopy image sequences

   https://doi.org/10.1117/12.2655627  

   Dave, Palak; Kolinko, Yaroslav; Morera, Hunter; Allen, Kurtis; Alahmari, Saeed; Goldgof, Dmitry; Hall, Lawrence O.; Mouton, Peter R. (April 2023, Proceedings of the SPIE, Volume 12471, id. 124710R 7 pp. (2023).)

   Tomaszewski, John E.; Ward, Aaron D. (Ed.)

   Automatic cell quantification in microscopy images can accelerate biomedical research. There has been significant progress in the 3D segmentation of neurons in fluorescence microscopy. However, it remains a challenge in bright-field microscopy due to the low Signal-to-Noise Ratio and signals from out-of-focus neurons. Automatic neuron counting in bright-field z-stacks is often performed on Extended Depth of Field images or on only one thick focal plane image. However, resolving overlapping cells that are located at different z-depths is a challenge. The overlap can be resolved by counting every neuron in its best focus z-plane because of their separation on the z-axis. Unbiased stereology is the state-of-the-art for total cell number estimation. The segmentation boundary for cells is required in order to incorporate the unbiased counting rule for stereology application. Hence, we perform counting via segmentation. We propose to achieve neuron segmentation in the optimal focal plane by posing the binary segmentation task as a multi-class multi-label task. Also, we propose to efficiently use a 2D U-Net for inter-image feature learning in a Multiple Input Multiple Output system that poses a binary segmentation task as a multi-class multi-label segmentation task. We demonstrate the accuracy and efficiency of the MIMO approach using a bright-field microscopy z-stack dataset locally prepared by an expert. The proposed MIMO approach is also validated on a dataset from the Cell Tracking Challenge achieving comparable results to a compared method equipped with memory units. Our z-stack dataset is available at 

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