CellPath-Bench is a new benchmark that evaluates whole-slide cellular representations in pathology foundation models (PFMs) by using 25 spatially aligned H&E–Xenium tissue sections from 11 organs and over 7 million cells. It introduces metrics such as Cell Representation Advantage (CRA) and Cell Representation Transferability (CRT) to assess how well frozen PFMs encode cell-type information and generalize across tissue sections, datasets, and organs. The benchmark was applied to 30 PFMs, revealing significant model-dependent differences in cell-type decodability and cross-domain generalization, and offers a standardized framework for auditing cellular information in frozen PFM representations.
By Bokai Zhao, Yiyang Zhang, Hanqing Chao, Yawei Ma, Long Bai, Tai Ma, Minfeng Xu, Ming Song, Tianzi Jiang
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)
arXiv:2608. 09636v1 Announce Type: cross Abstract: Accurate 3D neuron segmentation in fluorescence microscopy is critical for neuroscience.
By Haiyang Yan, Jinyue Guo, Yanchao Zhang, Bingqing Wang, Zhenchen Li, Jing Liu, Jiazheng Liu, Linlin Li, Hua Han
Catena is an open‑source, developer‑centric software suite designed to streamline large‑scale connectomics from electron microscopy data. It integrates modules for 3D neuron and organelle segmentation, synapse detection, microtubule tracking, and neurotransmitter inference into composable, chunk‑wise pipelines that are fully documented and extensible. The suite includes pretrained machine learning models, containerized runtimes, and shareable components to reduce compute and ground‑truth data needs while ensuring reproducible, scalable processing across workstations and clusters.
By Samia Mohinta, Pedro G\'omez-G\'alvez, Shi Yan Lee, Daniel Franco-Barranco, Michael Clayton, Stephan Preibisch, Jan Funke, Albert Cardona
Tracking neurite morphology over time helps characterize structural changes during neuronal development and deterioration, but long-term time-lapse imaging is resource-intensive and difficult to scale...
arXiv:2609.23990v1 Announce Type: new
Abstract: Tracking neurite morphology over time helps characterize structural changes during neuronal development and deterioration, but long-term time-lapse ima...
By Tsung Yeh Hsieh, Cosmin Anitescu, Chunghwan Kim, Victoria A. Webster-Wood, Yongjie Jessica Zhang
The paper introduces RABR-Net, a two‑stage framework that refines biomedical image segmentation boundaries by combining multiple uncertainty measures into a boundary‑aware representation. A gated residual refiner uses this representation to selectively correct uncertain boundary pixels while preserving confident regions, leading to modest but statistically significant improvements in Dice, Boundary Dice, and HD95 metrics on a held‑out test set. Qualitative results show the refiner focuses on uncertain cytoplasm and nucleus boundaries, though calibration does not automatically improve.
By Anima Kujur
arXiv:2607. 16065v1 Announce Type: cross Abstract: Retinal layer segmentation in Optical Coherence Tomography (OCT) is a fundamental step for extracting quantitative biomarkers of retinal structure.
By Iker Moran-Cavero, Monica Hernandez, Elvira Mayordomo, Naiara Artiaga, Beatriz Pardi\~nas, Beatriz Cordon, Elena Garcia-Martin
arXiv:2608.30768v1 Announce Type: new
Abstract: Automatic neuron reconstruction from light microscopy images is a central problem in computational neuroanatomy. While recent methods have achieved enc...
By Zekang Yang, Jiamin Li, Zhenghua Li, Jiaqi Fan, Zengcai Guo, Xiaolin Hu
arXiv:2606. 10255v1 Announce Type: cross Abstract: Cryo-electron tomography (cryoET) has emerged as a powerful tool in structural and cellular biology by enabling direct visualization of macromolecular structures within intact cells, thereby linking molecular architecture to cellular organization in a native context.
By Jonathan Schwartz, Utz Heinrich Ermel, C. Braxton Owens, Zhuowen Zhao, Ariana Peck, Gus L. W. Hart, Grant J. Jensen, Bridget Carragher, Dari Kimanius
arXiv:2608. 07575v1 Announce Type: cross Abstract: Confocal microscopy of optically cleared and swelled tissue resolves complex biological structures in 3D, but such acquisitions are highly anisotropic: along the under-sampled axial direction the structure can appear discontinuous, hampering reconstruction and automated quantitative analysis.
By Arash Fatehi, Robin Ebbestad, Linus Butt, Hans Blom, Sigrid Lundberg, Hannes Olauson, Hjalmar Brismar, David Unnersj\"o-Jess, Thomas Benzing, Katarzyna Bozek
arXiv:2609.31431v1 Announce Type: new
Abstract: Accurate segmentation of axons in 3D microscopy data is important for analyzing white-matter organization, but dense ground truth labels are expensive...
By Edward Gaibor, Kyriaki-Margarita Bintsi, Carmen Luz Leiva Ureta, Zayneb Bellatif, Chiara Maffei, Wenze Li, Elizabeth Hillman, Ya\"el Balbastre, Anastasia Yendiki