arXiv AI

QCell: Recombining and Aligning Cell Queries for Overlapping Instance Segmentation

QCell is a query‑based model designed to improve overlapping cell instance segmentation in microscopy images. It introduces an instance recombination module that decomposes and recombines query representations in latent space, allowing the model to reason about entire cell structures even when they overlap. Additionally, a contrastive query alignment objective is used to learn distinctive instance features and separate overlapping cell queries. The authors also present a new Organoid dataset benchmark and demonstrate that QCell surpasses state‑of‑the‑art methods, achieving +2.2 AP and +2.7 AJI on the ISBI2014 benchmark.

arXiv AI
Sep 15

End-to-End Cell Detection via Instance-aware Graph Modeling

The paper introduces an end‑to‑end framework for detecting and classifying cells in pathology images by jointly modeling visual features and instance‑level interactions. It employs a dynamic graph construction module that builds cell graphs from learnable queries and an instance‑aware graph network that filters and reorganizes features, integrating appearance and relational evidence. Experiments on multiple staining protocols show the method surpasses existing approaches in both detection and classification accuracy.

By Ruochen Liu, Yalin Zheng, Jingxin Liu, Jianfeng Zhang, Shoujun Huang, Dexing Kong, Haofeng Li, Wei Lou
arXiv Computer Vision
Sep 18

Scene-Q: Confidence-Aware Coarse-to-Fine Querying of 3D Scenes with Selective VLM Reasoning

Scene-Q is a confidence‑aware, coarse‑to‑fine querying framework for indoor mobile robots that grounds natural‑language queries in a 3D map. It normalizes encoder scores with temperature scaling and only invokes a reasoning VLM for low‑confidence cases, while high‑confidence queries are answered by fast retrieval. The method improves open‑vocabulary 3D instance segmentation on ScanNet200 and natural‑language 3D instance retrieval on real‑world reconstructions, especially for spatial and relational queries, while maintaining a substantial fraction of queries on the fast path.

By Juno Kim, Yesol Park, Hye-Jung Yoon, Byoung-Tak Zhang
arXiv Machine Learning
Jul 8

Conformal Prediction Sets for Instance Segmentation

arXiv:2602. 10045v2 Announce Type: replace-cross Abstract: Current instance segmentation models achieve high performance on average predictions, but lack principled uncertainty quantification: their outputs are not calibrated, and there is no guarantee that a predicted mask is close to the ground truth.

By Kerri Lu, Dan M. Kluger, Stephen Bates, Sherrie Wang
arXiv AI
Jul 28

scMIR: a vision-language foundation model for single-cell light microscopy image representation

arXiv:2607. 22712v1 Announce Type: cross Abstract: Single-cell light microscopy images have become an important data source for characterizing cell phenotypes, but their complexity and heterogeneity pose challenges to high-throughput automated analysis.

By Yifan Shang (Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China, College of Computer Science and Electronic Engineering, Hunan University, Changsha, China), Jiahui Tan (College of Computer Science and Electronic Engineering, Hunan University, Changsha, China), Xiangxiang Zeng (College of Computer Science and Electronic Engineering, Hunan University, Changsha, China), Renjie Zhou (Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China)
Hugging Face Trending Papers
Aug 3

SpatialQuery: Benchmarking Geometry-Grounded Multi-Instance Spatial Reasoning in Vision-Language Models

Vision-language models (VLMs) achieve strong semantic understanding but remain unreliable in metric spatial reasoning, particularly when queries require comparing multiple instances of the same object category. We study this problem through the Closest-Instance Distance Query (CIDQ), where a model must identify the nearest visible candidate to a unique reference object and estimate their gravity-aligned floor-plane distance.