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1. Local shape descriptors for neuron segmentation

   https://doi.org/10.1038/s41592-022-01711-z  

   Sheridan, Arlo; Nguyen, Tri M.; Deb, Diptodip; Lee, Wei-Chung Allen; Saalfeld, Stephan; Turaga, Srinivas C.; Manor, Uri; Funke, Jan (February 2023, Nature Methods)

   Abstract We present an 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 capture local statistics about the neuron to be segmented, such as diameter, elongation, and direction. On a study comparing several existing methods across various specimen, imaging techniques, and resolutions, 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), while being two orders of magnitudes more efficient—a critical requirement for the processing of future petabyte-sized datasets. 

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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. 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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4. Local Temperature Scaling for Probability Calibration

   https://doi.org/10.1109/ICCV48922.2021.00681  

   Ding, Zhipeng; Han, Xu; Liu, Peirong; Niethammer, Marc (October 2021, International Conference on Computer Vision)

   For semantic segmentation, label probabilities are often uncalibrated as they are typically only the by-product of a segmentation task. Intersection over Union (IoU) and Dice score are often used as criteria for segmentation success, while metrics related to label probabilities are not often explored. However, probability calibration approaches have been studied, which match probability outputs with experimentally observed errors. These approaches mainly focus on classification tasks, but not on semantic segmentation. Thus, we propose a learning-based calibration method that focuses on multi-label semantic segmentation. Specifically, we adopt a convolutional neural network to predict local temperature values for probability calibration. One advantage of our approach is that it does not change prediction accuracy, hence allowing for calibration as a postprocessing step. Experiments on the COCO, CamVid, and LPBA40 datasets demonstrate improved calibration performance for a range of different metrics. We also demonstrate the good performance of our method for multi-atlas brain segmentation from magnetic resonance images. 

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5. Make the Pertinent Salient: Task-Relevant Reconstruction for Visual Control with Distractions

   Kim, Kyungmin Kim; Lanier, JB; Fox, Roy (August 2025, RLJ)

   Model-Based Reinforcement Learning (MBRL) has shown promise in visual control tasks due to its data efficiency. However, training MBRL agents to develop generalizable perception remains challenging, especially amid visual distractions that introduce noise in representation learning. We introduce Segmentation Dreamer (SD), a framework that facilitates representation learning in MBRL by incorporating a novel auxiliary task. Assuming that task-relevant components in images can be easily identified with prior knowledge in a given task, SD uses segmentation masks on image observations to reconstruct only task-relevant regions, reducing representation complexity. SD can leverage either ground-truth masks available in simulation or potentially imperfect segmentation foundation models. The latter is further improved by selectively applying the image reconstruction loss to mitigate misleading learning signals from mask prediction errors. In modified DeepMind Control suite and Meta-World tasks with added visual distractions, SD achieves significantly better sample efficiency and greater final performance than prior work and is especially effective in sparse reward tasks that had been unsolvable by prior work. We also validate its effectiveness in a real-world robotic lane-following task when training with intentional distractions for zero-shot transfer.a 

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