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Ultra-fast processing of gigapixel Tissue MicroArray images using high performance computing

Yinhai Wang, David McCleary, Ching-Wei Wang, Paul Kelly, Jackie James, Dean A Fennell, Peter Hamilton
2010 Analytical Cellular Pathology  
analysis platform for TMA biomarker discovery that will significantly enhance the reliability and speed for biomarker research.  ...  The processing of such slides is time-consuming, bottlenecking a potentially high throughput platform. a High Performance Computing (HPC) platform for the rapid analysis of TMA virtual slides is presented  ...  platform for biomarker discovery in tissues.  ... 
doi:10.3233/acp-clo-2010-0551 pmid:21127378 pmcid:PMC4605732 fatcat:da5sjzmrgrctxh4rfqgvl6e64a

Ultra-Fast Processing of Gigapixel Tissue MicroArray Images Using High Performance Computing

Yinhai Wang, David McCleary, Ching-Wei Wang, Paul Kelly, Jackie James, Dean A. Fennell, Peter Hamilton
2010 Analytical Cellular Pathology  
throughput analysis platform for TMA biomarker discovery that will significantly enhance the reliability and speed for biomarker research.  ...  Tissue MicroArrays (TMAs) are a valuable platform for tissue based translational research and the discovery of tissue biomarkers.  ...  platform for biomarker discovery in tissues.  ... 
doi:10.1155/2010/918306 fatcat:bxdr2upnabd3ro3tkwkvqob6km

Quantitative proteomic profiling of breast cancers using a multiplexed microfluidic platform for immunohistochemistry and immunocytochemistry

Minseok S. Kim, Seyong Kwon, Taemin Kim, Eun Sook Lee, Je-Kyun Park
2011 Biomaterials  
This result indicates that the microfluidic IHC/ ICC platform is useful for accurate histopathological diagnoses using numerous specific biomarkers simultaneously, facilitating the individualization of  ...  This paper describes a multiplexed microfluidic immunohistochemistry (IHC)/immunocytochemistry (ICC) platform for quantitative proteomic profiling in breast cancer samples.  ...  (A) An image being aligned between the device and the cell block after the blocking process. (B) A stained image showing that the microfluidic massive ICC process was finished.  ... 
doi:10.1016/j.biomaterials.2010.10.040 pmid:21093044 fatcat:5gtddtxnrzcmni4q2pdd6tan7e

PRIMAGE project: predictive in silico multiscale analytics to support childhood cancer personalised evaluation empowered by imaging biomarkers

Luis Martí-Bonmatí, Ángel Alberich-Bayarri, Ruth Ladenstein, Ignacio Blanquer, J. Damian Segrelles, Leonor Cerdá-Alberich, Polyxeni Gkontra, Barbara Hero, J. M. García-Aznar, Daniel Keim, Wolfgang Jentner, Karine Seymour (+22 others)
2020 European Radiology Experimental  
The open cloud-based platform will offer precise clinical assistance for phenotyping (diagnosis), treatment allocation (prediction), and patient endpoints (prognosis), based on the use of imaging biomarkers  ...  PRIMAGE is one of the largest and more ambitious research projects dealing with medical imaging, artificial intelligence and cancer treatment in children.  ...  Acknowledgements PRIMAGE (PRedictive In-silico Multiscale Analytics to support cancer personalised diaGnosis and prognosis, empowered by imaging biomarkers) Business Place is a Horizon 2020 | RIA (Topic  ... 
doi:10.1186/s41747-020-00150-9 pmid:32246291 fatcat:qujua7cvcnbvvelwuolpaygduu

Highly Sensitive Direct Quantification of Cf-miRNAs for Biomarker Profiling by Next Generation Sequencing (NGS)

Sergio Barberan-Soler, Quincy Okobi, Van Lau, Brian H Johnston, Sergei A Kazakov
2019 Journal of Biomolecular Techniques  
With these new capabilities, the RealSeq platform should advance the prospects of cf-miRNAs as clinical biomarkers.  ...  biomarkers via NGS-based detection compared to circulating DNA and protein markers.  ...  With these new capabilities, the RealSeq platform should advance the prospects of cf-miRNAs as clinical biomarkers. 59 Imaging in Developmental Biology: An Essential Tool with No Instructions Guillermo  ... 
pmid:31892887 pmcid:PMC6936892 fatcat:4pzr7qd2pfblxgv7e2iv4wk46a

Breast Cancer Diagnosis Using a Microfluidic Multiplexed Immunohistochemistry Platform

Minseok S. Kim, Taemin Kim, Sun-Young Kong, Soim Kwon, Chae Yun Bae, Jaekyu Choi, Chul Hwan Kim, Eun Sook Lee, Je-Kyun Park, Syed A. Aziz
2010 PLoS ONE  
However, there is no suitable IHC platform for multiplex assay toward personalized cancer therapy.  ...  Biomarkers play a key role in risk assessment, assessing treatment response, and detecting recurrence and the investigation of multiple biomarkers may also prove useful in accurate prediction and prognosis  ...  Acknowledgments The authors gratefully acknowledge Bumi Kwon for making cell blocks, Seyong Kwon for experimental assistance and Jaeduck Jang for image analysis. Author Contributions  ... 
doi:10.1371/journal.pone.0010441 pmid:20454672 pmcid:PMC2862720 fatcat:xw52uaz7lrhubdlei3at7kd5c4

ePAD: An Image Annotation and Analysis Platform for Quantitative Imaging

2019 Tomography  
We present an overview of ePAD as a platform for medical image annotation and quantitative analysis.  ...  Quantitative lesion assessment on images is time-consuming, and adopting new promising quantitative imaging biomarkers of response in clinical trials is challenging.  ...  We created the QIFP, a cloud-based platform for building processing pipelines of image analysis algorithms (88) .  ... 
doi:10.18383/j.tom.2018.00055 pmid:30854455 pmcid:PMC6403025 fatcat:uyusdmfkzzgp7gjgx2c23p4liq

A cloud infrastructure for scalable computing on population imaging databanks

Ignacio Blanquer, Miguel Caballer, Luis Martí Bonmatí, Ángel Alberich Bayarri, María De la Iglesia, Jacobo Martínez
2015 International Journal of Image Mining  
This article describes the software architecture designed to cope with the computing demand of research usage of complex data from the imaging biobank of the Regional Ministry of Health in the Valencia  ...  deploy virtual elastic clusters that adjust themselves to the actual workload of the study, therefore reducing operating costs and preventing the need of up-front investments both at the level of the imaging  ...  His main research interests include radiology, imaging biomarkers, imaging processing, abdominal imaging and magnetic resonance imaging.  ... 
doi:10.1504/ijim.2015.073015 fatcat:4fiugziw5nb5pa5bje7geeznkq

CORBEL Report on final assessment and generalization of integration platform

Jan-Willem Boiten, Silvio Aime, Mariska Bierkens, Walter Dastrù, Mattias Hansson, Stefan Klein, Dario Longo, Sjaak Peelen, Sara Zullino, Luca Sangiorgi, Marina Mordenti, Manila Boarini (+1 others)
2020 Zenodo  
, importing, archiving preclinical studies based on magnetic resonance imaging (MRI) from several vendors, including tools for automated image processing.  ...  Task 3.4 in CORBEL ("Data integration and management services for image-driven and genomicsdriven biomarker studies") was designed to develop a common IT framework to support data handling and analysis  ...  The core of the CORBEL common IT framework for genomics and imaging studies in biomarker research consists of the tranSMART (data integration and browsing platform), cBioportal (patientlevel genomics platform  ... 
doi:10.5281/zenodo.3628369 fatcat:o4h7ygkx6zdbpeqptc6s4nn4vq

The Role of Digital Biomarkers in Cancer Research and Patient Care

Severin Rodler
2019 Biomedical Journal of Scientific & Technical Research  
While previous works have focused on the role of digital biomarkers in cardiovascular and neurological diseases, we aim to address the role of digital biomarkers in cancer research.  ...  ARTICLE INFO abstract Classical biomarkers have been traditionally used to evaluate changes in the homeostasis of the human body.  ...  Current Digital Biomarker Landscape in Cancer Research and Patient Care Digital biomarkers can be generated from various sources like body sensors, image processing or from health platforms and electronic  ... 
doi:10.26717/bjstr.2019.17.003009 fatcat:zq4wx66s6regre2fghi7uwpa5q

P01.04 A spatially resolved, highly multiplexed biomarker analysis pipeline that bridges the divide between discovery and clinical research

O Braubach, M Gallina, B Remeniuk, C Wang, N Nikulina, R Bashier, J Kennedy-Darling, C Hoyt
2020 Journal for ImmunoTherapy of Cancer  
Image processing and data analysis were conducted similarly for both datasets so that repeatability and consistency of measurements could be established.ResultsBoth CODEX® and Phenoptics™ detected the  ...  comparison provides a conceptual framework for biomarkers discovered on the CODEX® platform to be translated to the Phenoptics™ platform for high-throughput translational studies.  ...  Image processing and data analysis were conducted similarly for both datasets so that repeatability and consistency of measurements could be established.  ... 
doi:10.1136/jitc-2020-itoc7.17 fatcat:dhuxjqi2xrdf5mm5tdrux27k7q

Computational Radiomics System to Decode the Radiographic Phenotype

Joost J.M. van Griethuysen, Andriy Fedorov, Chintan Parmar, Ahmed Hosny, Nicole Aucoin, Vivek Narayan, Regina G.H. Beets-Tan, Jean-Christophe Fillion-Robin, Steve Pieper, Hugo J.W.L. Aerts
2017 Cancer Research  
However, lack of standardized algorithm definitions and image processing severely hampers reproducibility and comparability of results.  ...  Radiomic artificial intelligence (AI) technology, either based on engineered hard-coded algorithms or deep learning methods, can be used to develop noninvasive imaging-based biomarkers.  ...  Grant Support The authors acknowledge financial support from the Informatics Technology for Cancer Research (ITCR) program (NIH-USA U24CA194354) and the Quantitative Imaging Network (QIN) program (NIH-USA  ... 
doi:10.1158/0008-5472.can-17-0339 pmid:29092951 fatcat:6jxdhwg6mjfzddngj4ymakqydi

NEW PRODUCTS

2008 Science  
The new platform complements MASStermind, a biomarker discovery platform capable of generating a high quality hit list of low-abundance protein biomarkers in blood.  ...  Protein Biomarker Verification Platform MASSterclass is a sensitive protein biomarker verification tool that addresses a key bottleneck in biomarker development by enabling large-scale screening of biomarker  ... 
doi:10.1126/science.321.5885.144 fatcat:eqj4k6eq2vcvhlehi77sgnfnzm

Corbel Robust Data Upload Procedures For Biosample Data And Molecular Profiling Data

Jan-Willem Boiten, Mariska Bierkens, Matthias Hansson, Stefan Klein, Sjaak Peelen
2017 Zenodo  
platform) and XNAT (image archive platform) solutions.  ...  The core of the CORBEL common IT framework for genomics and imaging studies in biomarker research consists of the tranSMART (data integration and browsing platform), cBioportal (patient-level genomics  ...  ), cBioportal (patientlevel genomics platform) and XNAT (image archive platform) solutions.  ... 
doi:10.5281/zenodo.886507 fatcat:zrugjipjofhzresgq6ml5nt77u

Opportunities and challenges of disease biomarkers: a new section in the journal of translational medicine

Xiangdong Wang, Peter A Ward
2012 Journal of Translational Medicine  
substance that is an indicator of biological morphology, processes and function.  ...  Numerous imaging technologies have been applied for biomarker validation and development, including near infrared imaging, neuronuclear imaging, whole-body diffusion magnetic resonance imaging, specific  ... 
doi:10.1186/1479-5876-10-240 pmid:23217078 pmcid:PMC3543303 fatcat:rnuezcswnfckjagbbiukk4fjvq
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