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.

Gaussian Combined Distance: A Generic Metric for Object Detection

In object detection, a well-defined similarity metric can significantly enhance model performance. Currently, the IoU-based similarity metric is the most commonly preferred choice for detectors. However, detectors using IoU as a similarity metric often perform poorly when detecting small objects because of their sensitivity to minor positional deviations. To address this issue, recent studies have proposed the Wasserstein Distance as an alternative to IoU for measuring the similarity of Gaussian-distributed bounding boxes. However, we have observed that the Wasserstein Distance lacks scale invariance, which negatively impacts the model's generalization capability. Additionally, when used as a loss function, its independent optimization of the center attributes leads to slow model convergence and unsatisfactory detection precision. To address these challenges, we introduce the Gaussian Combined Distance (GCD). Through analytical examination of GCD and its gradient, we demonstrate that GCD not only possesses scale invariance but also facilitates joint optimization, which enhances model localization performance. Extensive experiments on the AI-TOD-v2 dataset for tiny object detection show that GCD, as a bounding box regression loss function and label assignment metric, achieves state-of-the-art performance across various detectors. We further validated the generalizability of GCD on the MS-COCO-2017 and Visdrone-2019 datasets, where it outperforms the Wasserstein Distance across diverse scales of datasets. Code is available at https://github.com/MArKkwanGuan/mmdet-GCD.