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Hyper-Stain Inspector: A Framework for Robust Registration and Localised Co-Expression Analysis of Multiple Whole-Slide Images of Serial Histology Sections

Nicholas Trahearn, David Epstein, Ian Cree, David Snead, Nasir Rajpoot
2017 Scientific Reports  
2017) Hyper-stain inspector : a framework for robust registration and localised co-expression analysis of multiple whole-slide images of serial histology sections. Scientific Reports, 7. 5641.  ...  Through cross-slide WSI registration, it becomes possible to select and analyse a common visual field across images of several serial section stained with different protein markers.  ...  Acknowledgements Whole-slide images used during the course of this project have been acquired using Omnyx scanners installed at University Hospitals Coventry and Warwickshire.  ... 
doi:10.1038/s41598-017-05511-w pmid:28717124 pmcid:PMC5514061 fatcat:d53tfyfmibglthh7w5sq6bk7mm

Automatic Multi-Stain Registration of Whole Slide Images in Histopathology [article]

Abubakr Shafique
2021 arXiv   pre-print
It requires cross-staining comparison among Whole Slide Images (WSIs) of immuno-histochemical and hematoxylin and eosin (H&E) microscopic slides.  ...  In addition to morphological deformations introduced during slide preparation, there are large variations in cell appearance and tissue morphology across different staining.  ...  Joint analysis of different IHC's are important to analyse any co-localised area, highlighting different useful information for the pathologists [6] .  ... 
arXiv:2107.14292v1 fatcat:4chkb3fasjfx3mrtcdbrrabgfa

Automated Histology Analysis: Opportunities for signal processing

Michael T McCann, John A. Ozolek, Carlos A. Castro, Bahram Parvin, Jelena Kovacevic
2015 IEEE Signal Processing Magazine  
One may also want to register images of two adjacent tissue slices that use different stains; e.g. H&E to IHC stains.  ...  Given serial sections of a tissue sample, each stained with H&E, one aim is to register them to create a tissue volume.  ...  She is a coauthor on an SP Society award-winning paper and is a coauthor of the textbooks "Wavelets and Subband Coding" and "Foundations of Signal Processing". Dr.  ... 
doi:10.1109/msp.2014.2346443 fatcat:ao6rczso3ndj7j2tw5p2vdywm4

Simultaneous automatic scoring and co-registration of hormone receptors in tumor areas in whole slide images of breast cancer tissue slides

Nicholas Trahearn, Yee Wah Tsang, Ian A. Cree, David Snead, David Epstein, Nasir Rajpoot
2016 Cytometry Part A  
Whole-slide images used during the course of this project have been acquired using Omnyx scanners installed at University Hospitals Coventry and Warwickshire.  ...  Nicholas Trahearn created the automated algorithms under supervision of Nasir Rajpoot. David Epstein contributed to the development of the approximate registration algorithm.  ...  For each case, the ER/PR sections were co-registered to a H&E slide in the case.  ... 
doi:10.1002/cyto.a.23035 pmid:28009468 fatcat:zvfo7govjrevfmni5bvpca2mre

Automated quantitative analysis of Ki-67 staining and HE images recognition and registration based on whole tissue sections in breast carcinoma

Min Feng, Yang Deng, Libo Yang, Qiuyang Jing, Zhang Zhang, Lian Xu, Xiaoxia Wei, Yanyan Zhou, Diwei Wu, Fei Xiang, Yizhe Wang, Ji Bao (+1 others)
2020 Diagnostic Pathology  
(IHC) images and their matched hematoxylin-eosin (HE) images, or did not accurately labelled each positive and negative cell with Ki-67 staining based on whole tissue sections (WTS).  ...  Our study demonstrates the enormous potential of automated quantitative analysis of Ki-67 staining and HE images recognition and registration based on WTS, and the automated scoring of Ki67 can thus successfully  ...  Acknowledgments We thank all the pathologists and software engineers for participating in this study, including the team of 36 pathologists who were from West China Clinical Medical College of Sichuan  ... 
doi:10.1186/s13000-020-00957-5 pmid:32471471 fatcat:ah6lb7e6dra37ckfautdn7vy2y

Virtual histological staining of unlabelled tissue-autofluorescence images via deep learning

Yair Rivenson, Hongda Wang, Zhensong Wei, Kevin de Haan, Yibo Zhang, Yichen Wu, Harun Günaydın, Jonathan E. Zuckerman, Thomas Chong, Anthony E. Sisk, Lindsey M. Westbrook, W. Dean Wallace (+1 others)
2019 Nature Biomedical Engineering  
kidney, liver and lung, and involving different types of stain, showed no major discordances.  ...  The histological analysis of tissue samples, widely used for disease diagnosis, involves lengthy and laborious tissue preparation.  ...  Methods For each tissue and stain type, an image dataset made up of co-registered autofluorescence images of label-free tissue samples and the corresponding brightfield histochemically stained tissue images  ... 
doi:10.1038/s41551-019-0362-y pmid:31142829 fatcat:zdykuiagvnehpndmg54x76gg4e

Towards automatic protein co-expression quantification in immunohistochemical TMA slides

Leslie Solorzano, Carla Pereira, Diana Martins, Raquel Almeida, Fatima Carneiro, Gabriela Almeida, Carla Oliveira, Carolina Wahlby
2020 IEEE journal of biomedical and health informatics  
We performed IHC analysis in consecutive TMA slides and compared the automated quantification with the pathologists' manual assessment.  ...  To explore protein co-expression, we constructed a modular image analysis pipeline to spatially align tissue microarray (TMA) image slides, evaluate alignment quality, define tumor regions, and ultimately  ...  ACKNOWLEDGMENT The authors thank Dina Leitão and Gilza Gonçalves for the technical support with TMA slides processing, Mário Seixas for technical support with TMA slides digitalization and Johan Öfverstedt  ... 
doi:10.1109/jbhi.2020.3008821 pmid:32750958 fatcat:c5mhh3j3xng5rfgtn7znazgafa

Development of Multigene Expression Signature Maps at the Protein Level from Digitized Immunohistochemistry Slides

Gregory J. Metzger, Stephen C. Dankbar, Jonathan Henriksen, Anthony E. Rizzardi, Nikolaus K. Rosener, Stephen C. Schmechel, Thomas J. Templeton
2012 PLoS ONE  
Areas of cancer for these expression level maps are defined by a pathologist on adjacent, co-registered H&E slides, allowing assessment of IHC statistics and heterogeneity within the diseased tissue.  ...  histologically interpretable tissue sections.  ...  with tissue handling.  ... 
doi:10.1371/journal.pone.0033520 pmid:22438942 pmcid:PMC3305321 fatcat:xzpvwf5h4ncj3oukehqkxui7v4

A methodological pipeline for serial-section imaging and tissue realignment for whole-brain functional and connectivity assessment

Lilia Mesina, Aaron A. Wilber, Benjamin J. Clark, Sutherland Dube, Alexis J. Demecha, Craig E.L. Stark, Bruce L. McNaughton
2016 Journal of Neuroscience Methods  
are co-registered with a corresponding image acquired during vibratome sectioning, and a 3-D representation of neural tracer (and other products) throughout the entire brain is generated.  ...  Brains were cut in the coronal plane, and an image of the block face was acquired. Wide-field fluorescent scans of whole sections were acquired and analyzed using Matlab software.  ...  Health Solutions Fellowships to AAW and BJC, MH099682 and AG049090 to AAW, a Natural Sciences and Engineering Council of Canada Fellowship to BJC, and an Alberta Innovates Health Solutions Graduate Studentship  ... 
doi:10.1016/j.jneumeth.2016.03.021 pmid:27039972 pmcid:PMC5695690 fatcat:hk2cdnxefnbx3abdjgxbtnuykm

Measuring Protein Expression in Tissue

Karen M. Gustashaw, Peyman Najmabadi, Steven J. Potts
2010 Laboratory medicine  
Whole Slide Brightfield Scanning With brightfield whole slide scanning, a stained histological section is placed on a motorized platform and scanned at 20X (or 40X) using a color line-scan camera.  ...  Image 3_Whole slide image and detail of human pancreas section stained with hematoxylin, DAB (Ki67) and Fast Red (Insulin).  ... 
doi:10.1309/lm8qu4sbnv2vsast fatcat:2rkmi3maqzhb5b56t7jjm5yzkm

Data integration from pathology slides for quantitative imaging of multiple cell types within the tumor immune cell infiltrate

Zhaoxuan Ma, Stephen L. Shiao, Emi J. Yoshida, Steven Swartwood, Fangjin Huang, Michael E. Doche, Alice P. Chung, Beatrice S. Knudsen, Arkadiusz Gertych
2017 Diagnostic Pathology  
Method: We developed a pipeline that combines immunohistochemistry (IHC) and digital image analysis. One slide was stained with pan-cytokeratin and CD45 and the other slide with CD8, CD4 and CD68.  ...  Bland-Altman plots and Pearson correlation were used to investigate differences between densities and counts of immune cell underneath the transferred versus manually annotated tumor masks.  ...  Availability of data and materials Please contact author for data requests. The authors do not have any conflicts of interest to disclose.  ... 
doi:10.1186/s13000-017-0658-8 pmid:28923066 pmcid:PMC5604347 fatcat:7tcwfey2unfbvms65vc5cs5f7a

De novo discovery of metabolic heterogeneity with immunophenotype-guided imaging mass spectrometry

Verena M. Prade, Thomas Kunzke, Annette Feuchtinger, Maria Rohm, Birgit Luber, Florian Lordick, Achim Buck, Axel Walch
2020 Molecular Metabolism  
performed on the very same tissue section of mouse pancreatic islets and on human gastric cancer tissue specimens.  ...  However, automated steps for multi-omics analyses and interpretation of histological images have not yet been implemented in mass spectrometry data analysis workflows.  ...  DECLARATION OF INTEREST The authors declare no conflicts of interest. APPENDIX A.  ... 
doi:10.1016/j.molmet.2020.01.017 pmid:32278304 pmcid:PMC7149754 fatcat:mp6qd4hhhbdazevxvn3zvipsn4

PathFlow-MixMatch for Whole Slide Image Registration: An Investigation of a Segment-Based Scalable Image Registration Method [article]

Joshua J. Levy, Christopher R. Jackson, Christian C. Haudenschild, Brock C. Christensen, Louis J. Vaickus
2020 bioRxiv   pre-print
In digital pathology, image registration aligns correspondent regions of tissue from different stereotactic viewpoints (e.g. subsequent deeper sections of the same tissue).  ...  We tested our technique by having a pathologist annotate landmarks from 13 pairs of differently stained liver biopsy slides, performing WSI and segment-based registration techniques, and comparing overall  ...  Results Experimental Design Our workflow was used to register thirteen pairs of H&E stained and Trichrome stained WSI of liver tissue (randomly selected from our WSI corpus) to derive paired and registered  ... 
doi:10.1101/2020.03.22.002402 fatcat:lzqfupl23rgeviwlxtpqiodl6i

Systems pathology by multiplexed immunohistochemistry and whole-slide digital image analysis

Sami Blom, Lassi Paavolainen, Dmitrii Bychkov, Riku Turkki, Petra Mäki-Teeri, Annabrita Hemmes, Katja Välimäki, Johan Lundin, Olli Kallioniemi, Teijo Pellinen
2017 Scientific Reports  
We present an mIHC platform combining fluorescent and chromogenic staining with automated whole-slide imaging and integrated whole-slide image analysis, enabling simultaneous detection of six protein markers  ...  We conclude that the open-source combination of 8-plex mIHC detection, whole-slide image acquisition and analysis provides a robust tool allowing quantitative, spatially resolved whole-slide tissue cytometry  ...  Bruun at Institute for Cancer Research, Oslo University Hospital, Norway for his expertise and fruitful discussions regarding multispectral imaging and image analysis.  ... 
doi:10.1038/s41598-017-15798-4 pmid:29138507 pmcid:PMC5686230 fatcat:smkuvtfz35g5xbp2xhbnr7dpje

Informatics

2013 Laboratory Investigation  
Neoplasms and autoimmune diseases accounted for a minority of cases.  ...  Conclusions: This is the largest series of HLH cases in adults. Acute EBV and bacterial infections followed by histoplasmosis were the most frequent diseases identified in this series.  ...  This is a great opportunity for automation and we report our evaluation of a newly available whole slide image (WSI) based image analysis (IA) system.  ... 
doi:10.1038/labinvest.2013.26 fatcat:ss6pcvtf6bam5aiptokfuudz2e
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