Deep learning in histopathology: the path to the clinic

J Van der Laak, G Litjens, F Ciompi - Nature medicine, 2021 - nature.com
Abstract Machine learning techniques have great potential to improve medical diagnostics,
offering ways to improve accuracy, reproducibility and speed, and to ease workloads for …

Unbiased spatial proteomics with single-cell resolution in tissues

A Mund, AD Brunner, M Mann - Molecular Cell, 2022 - cell.com
Mass spectrometry (MS)-based proteomics has become a powerful technology to quantify
the entire complement of proteins in cells or tissues. Here, we review challenges and recent …

A foundation model for clinical-grade computational pathology and rare cancers detection

E Vorontsov, A Bozkurt, A Casson, G Shaikovski… - Nature medicine, 2024 - nature.com
The analysis of histopathology images with artificial intelligence aims to enable clinical
decision support systems and precision medicine. The success of such applications …

Scaling vision transformers to gigapixel images via hierarchical self-supervised learning

RJ Chen, C Chen, Y Li, TY Chen… - Proceedings of the …, 2022 - openaccess.thecvf.com
Abstract Vision Transformers (ViTs) and their multi-scale and hierarchical variations have
been successful at capturing image representations but their use has been generally …

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

The Tabula Sapiens Consortium*, RC Jones… - Science, 2022 - science.org
Molecular characterization of cell types using single-cell transcriptome sequencing is
revolutionizing cell biology and enabling new insights into the physiology of human organs …

A pathology foundation model for cancer diagnosis and prognosis prediction

X Wang, J Zhao, E Marostica, W Yuan, J Jin, J Zhang… - Nature, 2024 - nature.com
Histopathology image evaluation is indispensable for cancer diagnoses and subtype
classification. Standard artificial intelligence methods for histopathology image analyses …

Universeg: Universal medical image segmentation

VI Butoi, JJG Ortiz, T Ma, MR Sabuncu… - Proceedings of the …, 2023 - openaccess.thecvf.com
While deep learning models have become the predominant method for medical image
segmentation, they are typically not capable of generalizing to unseen segmentation tasks …

A visual-language foundation model for computational pathology

MY Lu, B Chen, DFK Williamson, RJ Chen, I Liang… - Nature Medicine, 2024 - nature.com
The accelerated adoption of digital pathology and advances in deep learning have enabled
the development of robust models for various pathology tasks across a diverse array of …

Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning

NF Greenwald, G Miller, E Moen, A Kong, A Kagel… - Nature …, 2022 - nature.com
A principal challenge in the analysis of tissue imaging data is cell segmentation—the task of
identifying the precise boundary of every cell in an image. To address this problem we …

CODA: quantitative 3D reconstruction of large tissues at cellular resolution

AL Kiemen, AM Braxton, MP Grahn, KS Han, JM Babu… - Nature …, 2022 - nature.com
A central challenge in biology is obtaining high-content, high-resolution information while
analyzing tissue samples at volumes relevant to disease progression. We address this here …