Ge Yang

Yunpeng Xiao, Youpeng Zhao, Ge Yang

Morphology of mitochondria plays critical roles in mediating their physiological functions. Accurate segmentation of mitochondria from 3D electron microscopy (EM) images is essential to quantitative characterization of their morphology at the nanometer scale. Fully supervised deep learning models developed for this task achieve excellent performance but require substantial amounts of annotated data for training. However, manual annotation of EM images is laborious and time-consuming because of their large volumes, limited contrast, and low signal-to-noise ratios (SNRs). To overcome this challenge, we propose a semi-supervised deep learning model that segments mitochondria by leveraging the spatial continuity of their structural, morphological, and contextual information in both labeled and unlabeled images. We use random piecewise affine transformation to synthesize comprehensive and realistic mitochondrial morphology for augmentation of training data. Experiments on the EPFL dataset show that our model achieves performance similar as that of state-of-the-art fully supervised models but requires only ~20% of their annotated training data. Our semi-supervised model is versatile and can also accurately segment other spatially continuous structures from EM images. Data and code of this study are openly accessible at https://github.com/cbmi-group/MPP.

Yiming Huang, Guole Liu, Yaoru Luo et al.

The scarcity of annotated data, particularly for rare diseases, limits the variability of training data and the range of detectable lesions, presenting a significant challenge for supervised anomaly detection in medical imaging. To solve this problem, we propose a novel unsupervised method for medical image anomaly detection: Attention-Augmented Differentiable top-k Feature Adaptation (ADFA). The method utilizes Wide-ResNet50-2 (WR50) network pre-trained on ImageNet to extract initial feature representations. To reduce the channel dimensionality while preserving relevant channel information, we employ an attention-augmented patch descriptor on the extracted features. We then apply differentiable top-k feature adaptation to train the patch descriptor, mapping the extracted feature representations to a new vector space, enabling effective detection of anomalies. Experiments show that ADFA outperforms state-of-the-art (SOTA) methods on multiple challenging medical image datasets, confirming its effectiveness in medical anomaly detection.

Yaoru Luo, Guole Liu, Yuanhao Guo et al.

How deep neural networks (DNNs) learn from noisy labels has been studied extensively in image classification but much less in image segmentation. So far, our understanding of the learning behavior of DNNs trained by noisy segmentation labels remains limited. In this study, we address this deficiency in both binary segmentation of biological microscopy images and multi-class segmentation of natural images. We generate extremely noisy labels by randomly sampling a small fraction (e.g., 10%) or flipping a large fraction (e.g., 90%) of the ground truth labels. When trained with these noisy labels, DNNs provide largely the same segmentation performance as trained by the original ground truth. This indicates that DNNs learn structures hidden in labels rather than pixel-level labels per se in their supervised training for semantic segmentation. We refer to these hidden structures in labels as meta-structures. When DNNs are trained by labels with different perturbations to the meta-structure, we find consistent degradation in their segmentation performance. In contrast, incorporation of meta-structure information substantially improves performance of an unsupervised segmentation model developed for binary semantic segmentation. We define meta-structures mathematically as spatial density distributions and show both theoretically and experimentally how this formulation explains key observed learning behavior of DNNs.