Article
Multidisciplinary Sciences
Chris Gorman, Davide Punzo, Igor Octaviano, Steven Pieper, William J. R. Longabaugh, David A. Clunie, Ron Kikinis, Andrey Y. Fedorov, Markus D. Herrmann
Summary: The article introduces Slim, an open-source, web-based slide microscopy viewer that implements the DICOM standard to achieve interoperability. It showcases Slim as the viewer for the NCI Imaging Data Commons and demonstrates its capabilities in interactive visualization of different types of microscopy images using standard DICOMweb services. The article also highlights Slim's ability to collect standardized image annotations for machine learning models and interpret model inference results.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Yubraj Gupta, Carlos Costa, Eduardo Pinho, Luis Bastiao Silva
Summary: The development of biomedical imaging technology enables the digitization of hundreds of glass slides at once. While new technologies and modalities offer new diagnostic tools, the lack of interoperability among multivendor systems remains a challenge. This article proposes an automated DICOMization pipeline that efficiently transforms distinct proprietary microscope images into standard DICOM, addressing this issue and demonstrating feasibility and performance.
Article
Chemistry, Multidisciplinary
Noelia Vallez, Jose Luis Espinosa-Aranda, Anibal Pedraza, Oscar Deniz, Gloria Bueno
Summary: Microscopy scanners and AI techniques have advanced biomedicine, but challenges arise from the variety of digital file formats used. DICOM stands out as a standard that transcends internal image formats, but its clinical use is limited. This paper presents the first web viewer system that integrates WSI DICOM images and AI models, aiming to bridge the gap and improve CAD WSI processing tasks.
APPLIED SCIENCES-BASEL
(2023)
Review
Radiology, Nuclear Medicine & Medical Imaging
Marco Eichelberg, Klaus Kleber, Marc Kaemmerer
Summary: The article discusses specific cyber attacks on healthcare imaging networks, proposing security measures and considerations for implementation. It highlights the importance of deploying virus scanners on critical hospital systems and establishing long-term strategies with vendors for encryption and access rights. Standard integration profiles on certificate management and access rights in PACS environments could help facilitate cybersecurity measures.
ACADEMIC RADIOLOGY
(2021)
Article
Optics
Qiang Li, Xianming Liu, Kaige Han, Cheng Guo, Junjun Jiang, Xiangyang Ji, Xiaolin Wu
Summary: This paper proposes an effective learning-based method for autofocusing in WSI, which achieves accurate and high-speed autofocus without any optical hardware modifications. Experimental results demonstrate the superior autofocusing performance of our method compared to other related methods.
Article
Chemistry, Multidisciplinary
Stylianos Karagiannis, Emmanouil Magkos, Christoforos Ntantogian, Ricardo Cabecinha, Theofanis Fotis
Summary: Medical imaging is crucial in modern healthcare, and the DICOM standard has revolutionized the storage and transmission of medical images. However, the implementation and deployment of DICOM protocol face challenges due to incomplete understanding. This research presents an implementation of DICOM communication and a simulation system for conducting cybersecurity tests, providing valuable resources for medical imaging professionals, researchers, and developers.
APPLIED SCIENCES-BASEL
(2023)
Review
Pathology
Andrew John Evans, Nadia Depeiza, Shara-Gaye Allen, Kimone Fraser, Suzanne Shirley, Runjan Chetty
Summary: This paper discusses the experience of using whole slide imaging and video conferencing tools for distance pathology education during the COVID-19 pandemic, with teachers and students showing strong support and positive feedback for this teaching modality, indicating that whole slide imaging is an important tool for future distance education.
JOURNAL OF CLINICAL PATHOLOGY
(2021)
Article
Medical Laboratory Technology
Peter J. Schueffler, Evangelos Stamelos, Ishtiaque Ahmed, Vijay K. Yarlagadda, Orly Ardon, Matthew G. Hanna, Victor E. Reuter, David S. Klimstra, Meera Hameed
Summary: This study aims to define and quantify relevant performance metrics for efficient visualization of cases and slides in digital slide viewers. The study results show that performance metrics such as time to open a case, time to change a slide, and time to change a field of view contribute to improving the configuration of the viewer, leading to increased efficiency for pathologists in routine digital pathology.
ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE
(2022)
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
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
Computer Science, Artificial Intelligence
Ming Y. Lu, Richard J. Chen, Dehan Kong, Jana Lipkova, Rajendra Singh, Drew F. K. Williamson, Tiffany Y. Chen, Faisal Mahmood
Summary: Deep learning-based computational pathology algorithms show great potential in various tasks, but require large high-quality training data. Collaborative integration of medical data from multiple institutions can enhance model performance, although privacy concerns and data sharing complexities remain challenging.
MEDICAL IMAGE ANALYSIS
(2022)
Article
Health Care Sciences & Services
Rui Lebre, Eduardo Pinho, Rui Jesus, Luis Bastiao, Carlos Costa
Summary: The rapid growth and heterogeneity of data volume in healthcare, especially medical imaging, has led to the development of specialized information systems supported by the DICOM standard. Dicoogle, an extensible medical imaging archive server, emerges as a tool to overcome the challenges posed by the complexity of these ecosystems. It has become a fundamental enabling technology in collaborative and telehealthcare environments. This article provides an in-depth view of the Dicoogle ecosystem, its impact on the community, and its positioning in the medical imaging software field.
JOURNAL OF MEDICAL SYSTEMS
(2022)
Article
Biochemical Research Methods
Ning Li, Tao Lv, Yulin Sun, Xiuli Liu, Shaoqun Zeng, Xiaohua Lv
Summary: A high throughput slanted scanning WSI system was developed to acquire multi-layer image data simultaneously with the slide surface slanted relative to the focal plane. By moving the slide, image fusion helped avoid defocus blur and demonstrated high quality and fast imaging of cytological and histological slide specimens without aberration correction, showing potential for efficient application in digital pathology.
JOURNAL OF BIOPHOTONICS
(2021)
Article
Multidisciplinary Sciences
Petr Holub, Heimo Mueller, Tomas Bil, Luca Pireddu, Markus Plass, Fabian Prasser, Irene Schluender, Kurt Zatloukal, Rudolf Nenutil, Tomas Brazdil
Summary: Access to whole-slide images is crucial for the development of AI methods in pathology. The authors propose a model for privacy risk analysis and guidelines for safe sharing of WSI data.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Youqing Mu, H. R. Tizhoosh, Taher Dehkharghanian, Clinton J. V. Campbell
Summary: The goal of AI-based computational pathology is to generate compact representations of whole slide images (WSIs) capturing essential diagnostic information. This study explores trainable mechanisms to generate compact slide-level representations in bone marrow cytology using deep learning. The results show promising performance in WSI retrieval and classification tasks, indicating the potential of this method to improve diagnostics in hematology and support AI-assisted computational pathology approaches.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Filipi Pires, Carlos Costa, Paulo Dias
Summary: Advanced visualization of medical imaging and mixed reality technology hold great promise for clinical applications, but they still face challenges in terms of real-time performance and data compatibility. Further research and development are needed to fully utilize their potential and compare them with existing technologies.
JOURNAL OF DIGITAL IMAGING
(2021)
Article
Computer Science, Information Systems
Micael Pedrosa, Andre Zuquete, Carlos Costa
Summary: The paper discusses the balance between confidentiality and openness of healthcare data, proposing a pseudonymisation protocol to protect data and comply with relevant regulations.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2021)
Article
Multidisciplinary Sciences
Yubraj Gupta, Carlos Costa, Eduardo Pinho, Luis A. Bastiao Silva, Rainer Heintzmann
Summary: This article presents IMAGE-IN, an interactive web-based multidimensional viewer designed for confocal laser scanning microscopy and focused ion beam scanning electron microscopy data. The viewer provides intuitive interfaces and various viewing options, enabling the visualization and analysis of multidimensional datasets.
Proceedings Paper
Computer Science, Artificial Intelligence
Yubraj Gupta, Rodrigo E. D. Guerrero, Carlos Costa, Rui Jesus, Eduardo Pinho, Luis A. Bastiao Silva
Summary: Advancements in high-throughput technologies have enabled researchers to collect massive amounts of multidimensional datasets, which can be used for visualizing internal structures or developing analytic algorithms. This article describes the design and implementation of an interactive web-based tool for visualizing multidimensional microscope imaging data.
2022 26TH INTERNATIONAL CONFERENCE INFORMATION VISUALISATION (IV)
(2022)
Proceedings Paper
Computer Science, Information Systems
Tibcrio Baptista, Rui Jesus, Luis Bastiao Silva, Carlos Costa
Summary: The use of digital imaging in medicine is crucial for modern diagnosis and treatment, and cloud platforms offer great potential for remote access and collaboration. However, the performance limitations posed by high-resolution medical images have slowed down the adoption of cloud-ready environments. This study proposes a scalable cloud platform that can handle extreme medical imaging scenarios.
2022 27TH IEEE SYMPOSIUM ON COMPUTERS AND COMMUNICATIONS (IEEE ISCC 2022)
(2022)
Proceedings Paper
Computer Science, Information Systems
Rui Jesus, Yubraj Gupta, Luis Bastiao Silva, Carlos Costa
Summary: Digital technologies have transformed clinical pathology, improving workflow and promoting data sharing, but the lack of software standardization has hindered its adoption. This article proposes a cloud-based solution that efficiently supports the management and visualization of Z-stack images, while remaining vendor-neutral.
2022 27TH IEEE SYMPOSIUM ON COMPUTERS AND COMMUNICATIONS (IEEE ISCC 2022)
(2022)
Correction
Health Care Sciences & Services
Rui Lebre, Eduardo Pinho, Rui Jesus, Luis Bastiao, Carlos Costa
JOURNAL OF MEDICAL SYSTEMS
(2022)
Proceedings Paper
Engineering, Biomedical
Rui Jesus, Luis Bastiao Silva, Carlos Costa
Summary: The adoption of digital pathology is increasing, requiring better tools and workflows for decision support. However, the high resolution of images and the large number of pathology evaluations make the slide review process arduous. Therefore, the integration of artificial intelligence tools is needed to improve the annotation workflows.
2022 IEEE INTERNATIONAL SYMPOSIUM ON MEDICAL MEASUREMENTS AND APPLICATIONS (MEMEA 2022)
(2022)
Article
Health Care Sciences & Services
Rui Lebre, Eduardo Pinho, Rui Jesus, Luis Bastiao, Carlos Costa
Summary: The rapid growth and heterogeneity of data volume in healthcare, especially medical imaging, has led to the development of specialized information systems supported by the DICOM standard. Dicoogle, an extensible medical imaging archive server, emerges as a tool to overcome the challenges posed by the complexity of these ecosystems. It has become a fundamental enabling technology in collaborative and telehealthcare environments. This article provides an in-depth view of the Dicoogle ecosystem, its impact on the community, and its positioning in the medical imaging software field.
JOURNAL OF MEDICAL SYSTEMS
(2022)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Yubraj Gupta, Carlos Costa, Eduardo Pinho, Luis A. Bastiao Silva, Shibarjun Mandal, Ute Neugebauer
Summary: A proposed normalization pipeline converts different vendor formats into a standard DICOM structure, allowing access by healthcare professionals. This solution saves time and effort, efficiently utilizing memory space.
2021 IEEE 34TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS (CBMS)
(2021)
Proceedings Paper
Health Care Sciences & Services
Rui Lebre, Carlos Costa
Summary: Physicians currently rely on technological innovations for accurate diagnosis, with medical imaging playing a crucial role in clinical practice. However, the exponential growth of medical imaging data has presented challenges for PACS systems in terms of efficiency and storage capabilities. A decentralized architecture has been proposed to address these challenges and improve the distribution of medical images among healthcare practitioners.
2021 INTERNATIONAL CONFERENCE ON E-HEALTH AND BIOENGINEERING (EHB 2021), 9TH EDITION
(2021)
Article
Computer Science, Information Systems
Micael Pedrosa, Rui Lebre, Carlos Costa
Summary: The article proposes a distributed database consensus protocol designed to improve the performance of EHR insertion operations by reducing data contention through data isolation. It explores the personal and non-transferable nature of EHR while following GDPR guidelines for data protection.
