Large-scale EM Benchmark for Multi-Organelle Instance Segmentation in the Wild

Accurate instance-level segmentation of organelles in electron microscopy (EM) is critical for quantitative analysis of subcellular morphology and inter-organelle interactions. However, current benchmarks, based on small, curated datasets, fail to capture the inherent heterogeneity and large spatial context of in-the-wild EM data, imposing fundamental limitations on current patch-based methods. To address these limitations, we developed a large-scale, multi-source benchmark for multi-organelle instance segmentation, comprising over 100,000 2D EM images across variety cell types and five organelle classes that capture real-world variability. Dataset annotations were generated by our designed connectivity-aware Label Propagation Algorithm (3D LPA) with expert refinement. We further benchmarked several state-of-the-art models, including U-Net, SAM variants, and Mask2Former. Our results show several limitations: current models struggle to generalize across heterogeneous EM data and perform poorly on organelles with global, distributed morphologies (e.g., Endoplasmic Reticulum). These findings underscore the fundamental mismatch between local-context models and the challenge of modeling long-range structural continuity in the presence of real-world variability. The benchmark dataset and labeling tool will be publicly released soon.

RFAssigner: A Generic Label Assignment Strategy for Dense Object Detection

Label assignment is a critical component in training dense object detectors. State-of-the-art methods typically assign each training sample a positive and a negative weight, optimizing the assignment scheme during training. However, these strategies often assign an insufficient number of positive samples to small objects, leading to a scale imbalance during training. To address this limitation, we introduce RFAssigner, a novel assignment strategy designed to enhance the multi-scale learning capabilities of dense detectors. RFAssigner first establishes an initial set of positive samples using a point-based prior. It then leverages a Gaussian Receptive Field (GRF) distance to measure the similarity between the GRFs of unassigned candidate locations and the ground-truth objects. Based on this metric, RFAssigner adaptively selects supplementary positive samples from the unassigned pool, promoting a more balanced learning process across object scales. Comprehensive experiments on three datasets with distinct object scale distributions validate the effectiveness and generalizability of our method. Notably, a single FCOS-ResNet-50 detector equipped with RFAssigner achieves state-of-the-art performance across all object scales, consistently outperforming existing strategies without requiring auxiliary modules or heuristics.

Adaptive Paradigm Synergy: Can a Cross-Paradigm Objective Enhance Long-Tailed Learning?

Self-supervised learning (SSL) has achieved impressive results across several computer vision tasks, even rivaling supervised methods. However, its performance degrades on real-world datasets with long-tailed distributions due to difficulties in capturing inherent class imbalances. Although supervised long-tailed learning offers significant insights, the absence of labels in SSL prevents direct transfer of these strategies.To bridge this gap, we introduce Adaptive Paradigm Synergy (APS), a cross-paradigm objective that seeks to unify the strengths of both paradigms. Our approach reexamines contrastive learning from a spatial structure perspective, dynamically adjusting the uniformity of latent space structure through adaptive temperature tuning. Furthermore, we draw on a re-weighting strategy from supervised learning to compensate for the shortcomings of temperature adjustment in explicit quantity perception.Extensive experiments on commonly used long-tailed datasets demonstrate that APS improves performance effectively and efficiently. Our findings reveal the potential for deeper integration between supervised and self-supervised learning, paving the way for robust models that handle real-world class imbalance.