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Register a new userDistance Map Loss Penalty Term for Semantic Segmentation
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Convolutional neural networks for semantic segmentation suffer from low performance at object boundaries. In medical imaging, accurate representation of tissue surfaces and volumes is important for tracking of disease biomarkers such as tissue morphology and shape features. In this work, we propose a novel distance map derived loss penalty term for semantic segmentation. We propose to use distance maps, derived from ground truth masks, to create a penalty term, guiding the networks focus towards hard-to-segment boundary regions. We investigate the effects of this penalizing factor against cross-entropy, Dice, and focal loss, among others, evaluating performance on a 3D MRI bone segmentation task from the publicly available Osteoarthritis Initiative dataset. We observe a significant improvement in the quality of segmentation, with better shape preservation at bone boundaries and areas affected by partial volume. We ultimately aim to use our loss penalty term to improve the extraction of shape biomarkers and derive metrics to quantitatively evaluate the preservation of shape.
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Automatic building extraction from aerial imagery has several applications in urban planning, disaster management, and change detection. In recent years, several works have adopted deep convolutional neural networks (CNNs) for building extraction, since they produce rich features that are invariant against lighting conditions, shadows, etc. Although several advances have been made, building extraction from aerial imagery still presents multiple challenges. Most of the deep learning segmentation methods optimize the per-pixel loss with respect to the ground truth without knowledge of the context. This often leads to imperfect outputs that may lead to missing or unrefined regions. In this work, we propose a novel loss function combining both adversarial and cross-entropy losses that learn to understand both local and global contexts for semantic segmentation. The newly proposed loss function deployed on the DeepLab v3+ network obtains state-of-the-art results on the Massachusetts buildings dataset. The loss function improves the structure and refines the edges of buildings without requiring any of the commonly used post-processing methods, such as Conditional Random Fields. We also perform ablation studies to understand the impact of the adversarial loss. Finally, the proposed method achieves a relaxed F1 score of 95.59% on the Massachusetts buildings dataset compared to the previous best F1 of 94.88%.
Raster-scan optoacoustic mesoscopy (RSOM) is a powerful, non-invasive optical imaging technique for functional, anatomical, and molecular skin and tissue analysis. However, both the manual and the automated analysis of such images are challenging, because the RSOM images have very low contrast, poor signal to noise ratio, and systematic overlaps between the absorption spectra of melanin and hemoglobin. Nonetheless, the segmentation of the epidermis layer is a crucial step for many downstream medical and diagnostic tasks, such as vessel segmentation or monitoring of cancer progression. We propose a novel, shape-specific loss function that overcomes discontinuous segmentations and achieves smooth segmentation surfaces while preserving the same volumetric Dice and IoU. Further, we validate our epidermis segmentation through the sensitivity of vessel segmentation. We found a 20 $%$ improvement in Dice for vessel segmentation tasks when the epidermis mask is provided as additional information to the vessel segmentation network.
In semantic segmentation, we aim to train a pixel-level classifier to assign category labels to all pixels in an image, where labeled training images and unlabeled test images are from the same distribution and share the same label set. However, in an open world, the unlabeled test images probably contain unknown categories and have different distributions from the labeled images. Hence, in this paper, we consider a new, more realistic, and more challenging problem setting where the pixel-level classifier has to be trained with labeled images and unlabeled open-world images -- we name it open world semantic segmentation (OSS). In OSS, the trained classifier is expected to identify unknown-class pixels and classify known-class pixels well. To solve OSS, we first investigate which distribution that unknown-class pixels obey. Then, motivated by the goodness-of-fit test, we use statistical measurements to show how a pixel fits the distribution of an unknown class and select highly-fitted pixels to form the unknown region in each image. Eventually, we propose an end-to-end learning framework, known-region-aware domain alignment (KRADA), to distinguish unknown classes while aligning distributions of known classes in labeled and unlabeled open-world images. The effectiveness of KRADA has been verified on two synthetic tasks and one COVID-19 segmentation task.
Accurate estimation of the positions and shapes of microscale objects is crucial for automated imaging-guided manipulation using a non-contact technique such as optical tweezers. Perception methods that use traditional computer vision algorithms tend to fail when the manipulation environments are crowded. In this paper, we present a deep learning model for semantic segmentation of the images representing such environments. Our model successfully performs segmentation with a high mean Intersection Over Union score of 0.91.
Histopathology has played an essential role in cancer diagnosis. With the rapid advances in convolutional neural networks (CNN). Various CNN-based automated pathological image segmentation approaches have been developed in computer-assisted pathological image analysis. In the past few years, Transformer neural networks (Transformer) have shown the unique merit of capturing the global long distance dependencies across the entire image as a new deep learning paradigm. Such merit is appealing for exploring spatially heterogeneous pathological images. However, there have been very few, if any, studies that have systematically evaluated the current Transformer based approaches in pathological image segmentation. To assess the performance of Transformer segmentation models on whole slide images (WSI), we quantitatively evaluated six prevalent transformer-based models on tumor segmentation, using the widely used PAIP liver histopathological dataset. For a more comprehensive analysis, we also compare the transformer-based models with six major traditional CNN-based models. The results show that the Transformer-based models exhibit a general superior performance over the CNN-based models. In particular, Segmenter, Swin-Transformer and TransUNet, all transformer-based, came out as the best performers among the twelve evaluated models.
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