Shan Xiong

Jiabao Chen, Shan Xiong, Jialin Peng

Domain adaptive segmentation (DAS) is a promising paradigm for delineating intracellular structures from various large-scale electron microscopy (EM) without incurring extensive annotated data in each domain. However, the prevalent unsupervised domain adaptation (UDA) strategies often demonstrate limited and biased performance, which hinders their practical applications. In this study, we explore sparse points and local human preferences as weak labels in the target domain, thereby presenting a more realistic yet annotation-efficient setting. Specifically, we develop Prefer-DAS, which pioneers sparse promptable learning and local preference alignment. The Prefer-DAS is a promptable multitask model that integrates self-training and prompt-guided contrastive learning. Unlike SAM-like methods, the Prefer-DAS allows for the use of full, partial, and even no point prompts during both training and inference stages and thus enables interactive segmentation. Instead of using image-level human preference alignment for segmentation, we introduce Local direct Preference Optimization (LPO) and sparse LPO (SLPO), plug-and-play solutions for alignment with spatially varying human feedback or sparse feedback. To address potential missing feedback, we also introduce Unsupervised Preference Optimization (UPO), which leverages self-learned preferences. As a result, the Prefer-DAS model can effectively perform both weakly-supervised and unsupervised DAS, depending on the availability of points and human preferences. Comprehensive experiments on four challenging DAS tasks demonstrate that our model outperforms SAM-like methods as well as unsupervised and weakly-supervised DAS methods in both automatic and interactive segmentation modes, highlighting strong generalizability and flexibility. Additionally, the performance of our model is very close to or even exceeds that of supervised models.

Dafei Qiu, Shan Xiong, Jiajin Yi et al.

Accurate segmentation of organelle instances from electron microscopy (EM) images plays an essential role in many neuroscience researches. However, practical scenarios usually suffer from high annotation costs, label scarcity, and large domain diversity. While unsupervised domain adaptation (UDA) that assumes no annotation effort on the target data is promising to alleviate these challenges, its performance on complicated segmentation tasks is still far from practical usage. To address these issues, we investigate a highly annotation-efficient weak supervision, which assumes only sparse center-points on a small subset of object instances in the target training images. To achieve accurate segmentation with partial point annotations, we introduce instance counting and center detection as auxiliary tasks and design a multitask learning framework to leverage correlations among the counting, detection, and segmentation, which are all tasks with partial or no supervision. Building upon the different domain-invariances of the three tasks, we enforce counting estimation with a novel soft consistency loss as a global prior for center detection, which further guides the per-pixel segmentation. To further compensate for annotation sparsity, we develop a cross-position cut-and-paste for label augmentation and an entropy-based pseudo-label selection. The experimental results highlight that, by simply using extremely weak annotation, e.g., 15\% sparse points, for model training, the proposed model is capable of significantly outperforming UDA methods and produces comparable performance as the supervised counterpart. The high robustness of our model shown in the validations and the low requirement of expert knowledge for sparse point annotation further improve the potential application value of our model.

Shan Xiong, Jiabao Chen, Ye Wang et al.

Annotation-efficient segmentation of the numerous mitochondria instances from various electron microscopy (EM) images is highly valuable for biological and neuroscience research. Although unsupervised domain adaptation (UDA) methods can help mitigate domain shifts and reduce the high costs of annotating each domain, they typically have relatively low performance in practical applications. Thus, we investigate weakly supervised domain adaptation (WDA) that utilizes additional sparse point labels on the target domain, which require minimal annotation effort and minimal expert knowledge. To take full use of the incomplete and imprecise point annotations, we introduce a multitask learning framework that jointly conducts segmentation and center detection with a novel cross-teaching mechanism and class-focused cross-domain contrastive learning. While leveraging unlabeled image regions is essential, we introduce segmentation self-training with a novel instance-aware pseudo-label (IPL) selection strategy. Unlike existing methods that typically rely on pixel-wise pseudo-label filtering, the IPL semantically selects reliable and diverse pseudo-labels with the help of the detection task. Comprehensive validations and comparisons on challenging datasets demonstrate that our method outperforms existing UDA and WDA methods, significantly narrowing the performance gap with the supervised upper bound. Furthermore, under the UDA setting, our method also achieves substantial improvements over other UDA techniques.

Jiabao Chen, Shan Xiong, Jialin Peng

Domain adaptive segmentation (DAS) of numerous organelle instances from large-scale electron microscopy (EM) is a promising way to enable annotation-efficient learning. Inspired by SAM, we propose a promptable multitask framework, namely Prompt-DAS, which is flexible enough to utilize any number of point prompts during the adaptation training stage and testing stage. Thus, with varying prompt configurations, Prompt-DAS can perform unsupervised domain adaptation (UDA) and weakly supervised domain adaptation (WDA), as well as interactive segmentation during testing. Unlike the foundation model SAM, which necessitates a prompt for each individual object instance, Prompt-DAS is only trained on a small dataset and can utilize full points on all instances, sparse points on partial instances, or even no points at all, facilitated by the incorporation of an auxiliary center-point detection task. Moreover, a novel prompt-guided contrastive learning is proposed to enhance discriminative feature learning. Comprehensive experiments conducted on challenging benchmarks demonstrate the effectiveness of the proposed approach over existing UDA, WDA, and SAM-based approaches.