Review
Oncology
Paola Chiara Rizzo, Ilaria Girolami, Stefano Marletta, Liron Pantanowitz, Pietro Antonini, Matteo Brunelli, Nicola Santonicco, Paola Vacca, Nicola Tumino, Lorenzo Moretta, Anil Parwani, Swati Satturwar, Albino Eccher, Enrico Munari
Summary: This study aimed to identify common pitfalls in validation studies of whole-slide imaging (WSI) and suggest measures to address these challenges. The results showed that technical issues and diagnostic problems were encountered with WSI technology. Technical problems included slide scan failure, prolonged review time, and the need for higher image resolution. Diagnostic challenges involved grading dysplasia, reliable assessment of mitoses, identification of microorganisms, and defining the invasive front of tumors.
FRONTIERS IN ONCOLOGY
(2022)
Article
Computer Science, Artificial Intelligence
Quoc Dang Vu, Kashif Rajpoot, Shan E. Ahmed Raza, Nasir Rajpoot
Summary: Diagnostic, prognostic and therapeutic decision-making of cancer in pathology clinics can now be carried out based on analysis of multi-gigapixel tissue images, also known as whole-slide images (WSIs). Deep convolutional neural networks (CNNs) have been proposed to derive unsupervised WSI representations, but a major trade-off is the lack of interpretability. To address this, a handcrafted framework called Handcrafted Histological Transformer (H2T) is presented, which offers competitive performance and is faster than Transformer models.
MEDICAL IMAGE ANALYSIS
(2023)
Article
Engineering, Electrical & Electronic
Qiang Li, Xianming Liu, Junjun Jiang, Cheng Guo, Xiangyang Ji, Xiaolin Wu
Summary: This paper introduces a novel technique of deep autofocusing for whole slide imaging (WSI) in digital pathology. The deep autofocusing network (DAFNet) works with only two images taken at different focal distances, reducing the cost and time compared to traditional methods that require capturing a stack of images with varying focal distances for each tile of the target image. The experimental results demonstrate the refocusing capability of the DAFNet method.
IEEE TRANSACTIONS ON COMPUTATIONAL IMAGING
(2021)
Article
Oncology
Sanghoon Lee, Mohamed Amgad, Pooya Mobadersany, Matt McCormick, Brian P. Pollack, Habiba Elfandy, Hagar Hussein, David A. Gutman, Lee A. D. Cooper
Summary: HistomicsML2 is a software tool for training machine learning classifiers, guiding users to informative training examples and improving efficiency and performance. It can be used for developing classifiers for different cancer types or as a rapid annotation tool.
Article
Multidisciplinary Sciences
Philippe Weitz, Masi Valkonen, Leslie Solorzano, Circe Carr, Kimmo Kartasalo, Constance Boissin, Sonja Koivukoski, Aino Kuusela, Dusan Rasic, Yanbo Feng, Sandra Sinius Pouplier, Abhinav Sharma, Kajsa Ledesma Eriksson, Leena Latonen, Anne-Vibeke Laenkholm, Johan Hartman, Pekka Ruusuvuori, Mattias Rantalainen
Summary: The analysis of FFPE tissue sections stained with H & E or IHC is crucial for evaluating surgically resected breast cancer specimens. Computational pathology image analysis methods have made significant progress recently, but are limited by the scarcity of public datasets. This publication provides the largest publicly available dataset of matched WSIs of H & E and IHC-stained tissue sections from female breast cancer patients.
Article
Multidisciplinary Sciences
Kevin Yeh, Ishaan Sharma, Kianoush Falahkheirkhah, Matthew P. Confer, Andres C. Orr, Yen-Ting Liu, Yamuna Phal, Ruo-Jing Ho, Manu Mehta, Ankita Bhargava, Wenyan Mei, Georgina Cheng, John C. Cheville, Rohit Bhargava
Summary: Chemical imaging, especially mid-infrared spectroscopic microscopy, allows label-free biomedical analysis with high molecular sensitivity. However, its slow speed and poor image quality hinder its widespread adoption. A new microscope design overcomes these limitations by providing high-throughput recording, low noise, and high spatial resolution, enabling speckle-free, high-resolution imaging at theoretical limits.
NATURE COMMUNICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Satya Prasanna Mallick, K. S. Adithya, Ratul Sabui, Balu Babu Naidu, Ranjeet Singh, Harish Babu, Gajula Jagadeesh, K. M. Venkata Amaresh, Ram Gopal, Vandana Sharma
Summary: We propose a novel approach to whole slide imaging (WSI) using a low-cost, portable, fully enclosed scanner device that can be controlled wirelessly through an intuitive user interface on an iPad. The device incorporates features such as automatic slide loading, brightness control, and an autofocus algorithm.
IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT
(2023)
Review
Radiology, Nuclear Medicine & Medical Imaging
Wadha Alyami, Andre Kyme, Roger Bourne
Summary: Validating MRI techniques for tissue characterization and disease-related tissue alterations requires rigorous validation with ground truth information such as histology. Direct correlation methods between histology and MRI often fail due to spatial errors. Standard protocols for clinical tissue processing and histology-based pathology reporting can be modified to address some of these errors, without compromising the clinical process. This review summarizes the advantages and limitations of MRI validation techniques based on coregistration of MRI with whole-mount histology of tissue specimens.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2022)
Editorial Material
Optics
Yair Rivenson, Aydogan Ozcan
Summary: Deep learning can significantly increase the scanning speed of whole slide imaging in histology, which can further accelerate the adoption of digital pathology.
LIGHT-SCIENCE & APPLICATIONS
(2022)
Article
Optics
Ivy H. M. Wong, Yan Zhang, Zhenghui Chen, Lei Kang, Terence T. W. Wong
Summary: Microscopy with ultraviolet surface excitation (MUSE) is a promising slide-free imaging technique that improves the histopathology workflow. This study proposes the incorporation of MUSE with speckle illumination (MUSES) to achieve sharp imaging on thick and rough specimens with improved contrast. Experimental results demonstrate the potential of MUSES in providing histological images with spatial resolution of around 1 µm within 10 minutes.
PHOTONICS RESEARCH
(2022)
Article
Medicine, General & Internal
Oscar Demeulenaere, Adrien Bertolo, Sophie Pezet, Nathalie Ialy-Radio, Bruno Osmanski, Clement Papadacci, Mickael Tanter, Thomas Deffieux, Mathieu Pernot
Summary: This study demonstrates the potential of 3D ultrafast ultrasound localization microscopy (ULM) in mapping the whole-brain microvasculature and flow in vivo, providing unprecedented insights into the cerebral vascular system in mice models. The technology has the potential to become a major tool for clinical investigation of the cerebral microcirculation.
Article
Clinical Neurology
Liting Shi, Lin Shen, Junming Jian, Wei Xia, Ke-Da Yang, Yifu Tian, Jianghai Huang, Bowen Yuan, Liangfang Shen, Zhengzheng Liu, Jiayi Zhang, Rui Zhang, Keqing Wu, Di Jing, Xin Gao
Summary: This study investigates whether whole-slide imaging (WSI)-based deep learning can contribute new precision to the diagnosis of intracranial germinoma (IG), oligodendroglioma, and low-grade astrocytoma. The results show that WSI and deep learning models can accurately diagnose these tumors and improve the accuracy of pathologists. The use of our model can assist clinicians in providing patients with optimal and timely treatment options.
Article
Medicine, Research & Experimental
Joshua Doyle, Benjamin F. Green, Margaret Eminizer, Daniel Jimenez-Sanchez, Steve Lu, Elizabeth L. Engle, Haiying Xu, Aleksandra Ogurtsova, Jonathan Lai, Sigfredo Soto-Diaz, Jeffrey S. Roskes, Julie S. Deutsch, Janis M. Taube, Joel C. Sunshine, Alexander S. Szalay
Summary: Multiplex immunohistochemistry/immunofluorescence (mIHC/mIF) technology enables the evaluation of multiple protein expressions at single-cell resolution while preserving tissue architecture. Cross-registration of multiplex immunofluorescence images with additional imaging modalities and immunohistochemistry (IHC) can improve the quality of data by enhancing downstream processes such as cell segmentation. A fully automated process was designed to perform a hierarchical, parallelizable, and deformable registration of multiplexed digital whole-slide images (WSIs). Additionally, a pan-membrane immunohistochemical staining method was developed for improved cell segmentation.
LABORATORY INVESTIGATION
(2023)
Article
Chemistry, Multidisciplinary
Yan Zhang, Lei Kang, Ivy H. M. Wong, Weixing Dai, Xiufeng Li, Ronald C. K. Chan, Michael K. Y. Hsin, Terence T. W. Wong
Summary: CHAMP is a promising histological imaging method that enables high-throughput and label-free imaging of tissues with high resolution and processing speed. By unsupervised learning, CHAMP images can be transformed into virtually stained histological images, extracting significant cellular features with high accuracy.
Article
Medicine, General & Internal
Qingwu Wu, Jianning Chen, Yong Ren, Huijun Qiu, Lianxiong Yuan, Huiyi Deng, Yana Zhang, Rui Zheng, Haiyu Hong, Yueqi Sun, Xinyue Wang, Xuekun Huang, Chunkui Shao, Haotian Lin, Lanqing Han, Qintai Yang
Summary: This study aimed to establish an AI evaluation platform, AICEP 2.0, for the cellular phenotyping diagnosis of nasal polyps using whole-slide imaging (WSI), and explore the clinical significance of different phenotypes of nasal polyps. The results showed significant clinical differences among the four phenotypes of nasal polyps, with some correlations observed between the percentage of peripheral eosinophils and other cell types in tissue, indicating potential associations between different cell types.
Article
Biochemistry & Molecular Biology
Eun-Joon Lee, Prakash Rath, Jimei Liu, Dungsung Ryu, Lirong Pei, Satish K. Noonepalle, Austin Y. Shull, Qi Feng, N. Scott Litofsky, Douglas C. Miller, Douglas C. Anthony, Mark D. Kirk, John Laterra, Libin Deng, Hong-Bo Xin, Xinguo Wang, Jeong-Hyeon Choi, Huidong Shi
JOURNAL OF GENETICS AND GENOMICS
(2015)
Article
Medicine, Research & Experimental
Kyle J. Chambers, Douglas C. Anthony, Gregory W. Randolph, Christopher J. Hartnick, Edward G. Stopa, Phillip C. Song
Article
Clinical Neurology
James S. Nix, Jerad M. Gardner, Felipe Costa, Alexandre L. Soares, Fausto J. Rodriguez, Brian Moore, Maria Martinez-Lage, Sunita Ahlawat, Murat Gokden, Douglas C. Anthony
JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY
(2018)
Article
Pathology
Prakash Rath, Douglas C. Miller, N. Scott Litofsky, Douglas C. Anthony, Qi Feng, Craig Franklin, Lirong Pei, Alan Free, Jimei Liu, Mingqiang Ren, Mark D. Kirk, Huidong Shi
EXPERIMENTAL AND MOLECULAR PATHOLOGY
(2011)
Article
Computer Science, Interdisciplinary Applications
Dmitriy Shin, Gerald Arthur, Mihail Popescu, Dmitry Korkin, Chi-Ren Shyu
JOURNAL OF BIOMEDICAL INFORMATICS
(2014)
Article
Multidisciplinary Sciences
Feng Li, Olga V. Glinskii, Jianjun Zhou, Landon S. Wilson, Stephen Barnes, Douglas C. Anthony, Vladislav V. Glinsky
Article
Multidisciplinary Sciences
Orr Hadass, Brittany N. Tomlinson, Major Gooyit, Shanyan Chen, Justin J. Purdy, Jennifer M. Walker, Chunyang Zhang, Andrew B. Giritharan, Whitley Purnell, Christopher R. Robinson, Dmitriy Shin, Valerie A. Schroeder, Mark A. Suckow, Agnes Simonyi, Grace Y. Sun, Shahriar Mobashery, Jiankun Cui, Mayland Chang, Zezong Gu
Review
Pathology
Brad Bolon, Douglas C. Anthony, Mark Butt, David Dorman, Michael V. Green, Peter B. Little, William M. Valentine, Daniel Weinstock, James Yan, Robert C. Sills
TOXICOLOGIC PATHOLOGY
(2008)
Article
Oncology
Olga V. Glinskii, Sudha Sud, Valeri V. Mossine, Thomas P. Mawhinney, Douglas C. Anthony, Gennadi V. Glinsky, Kenneth J. Pienta, Vladislav V. Glinsky
Review
Pathology
Chunyu Cai, Douglas C. Anthony, Peter Pytel
Article
Anatomy & Morphology
Renee Stonebridge, Ross J. Taliano, Terra D. Velilla, Douglas C. Anthony
FRONTIERS IN NEUROANATOMY
(2020)
Article
Multidisciplinary Sciences
Xin He, Douglas C. Anthony, Zulmira Catoni, Weibiao Cao
Summary: The study revealed a low incidence of pulmonary tumor embolism (PTE), with radiological imaging studies failing to detect the majority of PTE cases despite advances in radiological techniques. The discrepancy between antemortem clinical and postmortem diagnosis has not significantly improved over the past 30 years.
Article
Oncology
Kim D. Johnson, Olga V. Glinskii, Valeri V. Mossine, James R. Turk, Thomas P. Mawhinney, Douglas C. Anthony, Carolyn J. Henry, Virginia H. Huxley, Gennadi V. Glinsky, Kenneth J. Pienta, Avraham Raz, Vladislav V. Glinsky