A survey of methods for 3D histology reconstruction

J Pichat, JE Iglesias, T Yousry, S Ourselin… - Medical image analysis, 2018 - Elsevier
Histology permits the observation of otherwise invisible structures of the internal topography
of a specimen. Although it enables the investigation of tissues at a cellular level, it is invasive …

[HTML][HTML] The emergence of pathomics

R Gupta, T Kurc, A Sharma, JS Almeida… - Current Pathobiology …, 2019 - Springer
Abstract Purpose of Review Our goal is to provide an overview of machine learning methods
and artificial intelligence in digital pathology image analysis. We also highlight novel …

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 …

[HTML][HTML] Virtual alignment of pathology image series for multi-gigapixel whole slide images

CD Gatenbee, AM Baker, S Prabhakaran… - Nature …, 2023 - nature.com
Interest in spatial omics is on the rise, but generation of highly multiplexed images remains
challenging, due to cost, expertise, methodical constraints, and access to technology. An …

ANHIR: automatic non-rigid histological image registration challenge

J Borovec, J Kybic, I Arganda-Carreras… - IEEE transactions on …, 2020 - ieeexplore.ieee.org
Automatic Non-rigid Histological Image Registration (ANHIR) challenge was organized to
compare the performance of image registration algorithms on several kinds of microscopy …

[HTML][HTML] Label-free automated three-dimensional imaging of whole organs by microtomy-assisted photoacoustic microscopy

TTW Wong, R Zhang, C Zhang, HC Hsu… - Nature …, 2017 - nature.com
Abstract Three-dimensional (3D) optical imaging of whole biological organs with
microscopic resolution has remained a challenge. Most versions of such imaging techniques …

Guidelines and evaluation of clinical explainable AI in medical image analysis

W Jin, X Li, M Fatehi, G Hamarneh - Medical image analysis, 2023 - Elsevier
Explainable artificial intelligence (XAI) is essential for enabling clinical users to get informed
decision support from AI and comply with evidence-based medical practice. Applying XAI in …

Tissue clearing and 3D reconstruction of digitized, serially sectioned slides provide novel insights into pancreatic cancer

AL Kiemen, AI Damanakis, AM Braxton, J He, D Laheru… - Med, 2023 - cell.com
Pancreatic cancer is currently the third leading cause of cancer death in the United States.
The clinical hallmarks of this disease include abdominal pain that radiates to the back, the …

The ACROBAT 2022 challenge: automatic registration of breast cancer tissue

P Weitz, M Valkonen, L Solorzano, C Carr… - Medical Image …, 2024 - Elsevier
The alignment of tissue between histopathological whole-slide-images (WSI) is crucial for
research and clinical applications. Advances in computing, deep learning, and availability of …

In situ characterization of the 3D microanatomy of the pancreas and pancreatic cancer at single cell resolution

A Kiemen, AM Braxton, MP Grahn, KS Han, JM Babu… - BioRxiv, 2020 - biorxiv.org
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest forms of cancer.
Accumulating evidence indicates the tumor microenvironment is highly associated with …