arXiv AI
Jul 21

CORE -- A Cell-Level Coarse-to-Fine Image Registration Engine for Multi-stain Image Alignment

arXiv:2511. 03826v4 Announce Type: replace-cross Abstract: Accurate and efficient registration of whole slide images (WSIs) is essential for high-resolution, nuclei-level analysis in multi-stained tissue slides.

By Esha Sadia Nasir, Behnaz Elhaminia, Mark Eastwood, Catherine King, Owen Cain, Lorraine Harper, Paul Moss, Dimitrios Chanouzas, David Snead, Nasir Rajpoot, Adam Shephard, Shan E Ahmed Raza
arXiv Computer Vision
Sep 3

AtlasPatch: Scalable Foundation Model-based Tissue Detection and Patch Extraction for Computational Pathology

AtlasPatch is a scalable, high‑throughput whole‑slide image preprocessing method that uses a foundation‑model‑based tissue detector operating at thumbnail resolution. By updating only 0.076% of the SAM2 model weights and leveraging a curated dataset of 30,000 thumbnail‑mask pairs, it generates accurate tissue masks and directly produces patch coordinates at the desired magnification, eliminating repeated patch‑level inference. The approach achieves 0.986 precision, is up to 16× faster than existing deep‑learning methods, and maintains downstream multiple‑instance learning performance across six slide‑level classification tasks.

By Ahmed Alagha, Christopher Leclerc, Yousef Kotp, Omar Metwally, Calvin Moras, Peter Rentopoulos, Ghodsiyeh Rostami, Bich Ngoc Nguyen, Jumanah Baig, Abdelhakim Khellaf, Vincent Quoc-Huy Trinh, Rabeb Mizouni, Hadi Otrok, Jamal Bentahar, Mahdi S. Hosseini
arXiv AI
Jun 17

SegTME-UNI2: A Foundation Model-Based Framework for Generalisable Multiclass Cell Segmentation and LLM-Driven Tumour Microenvironment Characterisation in Histopathology

arXiv:2606. 17702v1 Announce Type: cross Abstract: Characterising the tumour microenvironment (TME) from routine H&E-stained histology images requires simultaneous cell segmentation, feature extraction, and interpretable clinical reporting.

By Wan Siti Halimatul Munirah Wan Ahmad, Faris Syahmi Samidi, Mohammad Badal Ahmmed, Vimal Angela Thiviyanathan, Selvam James Thavaraj, Anwar P. P. Abdul Majeed