Benchmarking Fish Dataset and Evaluation Metric in Keypoint Detection -- Towards Precise Fish Morphological Assessment in Aquaculture Breeding

Accurate phenotypic analysis in aquaculture breeding necessitates the quantification of subtle morphological phenotypes. Existing datasets suffer from limitations such as small scale, limited species coverage, and inadequate annotation of keypoints for measuring refined and complex morphological phenotypes of fish body parts. To address this gap, we introduce FishPhenoKey, a comprehensive dataset comprising 23,331 high-resolution images spanning six fish species. Notably, FishPhenoKey includes 22 phenotype-oriented annotations, enabling the capture of intricate morphological phenotypes. Motivated by the nuanced evaluation of these subtle morphologies, we also propose a new evaluation metric, Percentage of Measured Phenotype (PMP). It is designed to assess the accuracy of individual keypoint positions and is highly sensitive to the phenotypes measured using the corresponding keypoints. To enhance keypoint detection accuracy, we further propose a novel loss, Anatomically-Calibrated Regularization (ACR), that can be integrated into keypoint detection models, leveraging biological insights to refine keypoint localization. Our contributions set a new benchmark in fish phenotype analysis, addressing the challenges of precise morphological quantification and opening new avenues for research in sustainable aquaculture and genetic studies. Our dataset and code are available at https://github.com/WeizhenLiuBioinform/Fish-Phenotype-Detect.

Revealing Hierarchical Structure of Leaf Venations in Plant Science via Label-Efficient Segmentation: Dataset and Method

Hierarchical leaf vein segmentation is a crucial but under-explored task in agricultural sciences, where analysis of the hierarchical structure of plant leaf venation can contribute to plant breeding. While current segmentation techniques rely on data-driven models, there is no publicly available dataset specifically designed for hierarchical leaf vein segmentation. To address this gap, we introduce the HierArchical Leaf Vein Segmentation (HALVS) dataset, the first public hierarchical leaf vein segmentation dataset. HALVS comprises 5,057 real-scanned high-resolution leaf images collected from three plant species: soybean, sweet cherry, and London planetree. It also includes human-annotated ground truth for three orders of leaf veins, with a total labeling effort of 83.8 person-days. Based on HALVS, we further develop a label-efficient learning paradigm that leverages partial label information, i.e. missing annotations for tertiary veins. Empirical studies are performed on HALVS, revealing new observations, challenges, and research directions on leaf vein segmentation.

Weakly Supervised Nuclei Segmentation via Instance Learning

Weakly supervised nuclei segmentation is a critical problem for pathological image analysis and greatly benefits the community due to the significant reduction of labeling cost. Adopting point annotations, previous methods mostly rely on less expressive representations for nuclei instances and thus have difficulty in handling crowded nuclei. In this paper, we propose to decouple weakly supervised semantic and instance segmentation in order to enable more effective subtask learning and to promote instance-aware representation learning. To achieve this, we design a modular deep network with two branches: a semantic proposal network and an instance encoding network, which are trained in a two-stage manner with an instance-sensitive loss. Empirical results show that our approach achieves the state-of-the-art performance on two public benchmarks of pathological images from different types of organs.