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Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images

Coleman R Harris, Eliot T McKinley, Joseph T Roland, Qi Liu, Martha J Shrubsole, Ken S Lau, Robert J Coffey, Julia Wrobel, Simon N Vandekar, Olga Vitek
<span title="2022-01-04">2022</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
We present clear slide-to-slide variation in the raw, unadjusted data, and show that many of the proposed normalization methods reduce this variation while preserving and improving the biological signal  ...  Results We implement and compare data transformations and normalization algorithms in multiplexed imaging data.  ...  Multiplexed imaging methods such as multiplexed immunofluorescence (MxIF) (Gerdes et al., 2013) , multiplexed immunohistochemistry (IHC) (Tsujikawa et al., 2017) and CODEX (Goltsev et al., 2018) are  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btab877">doi:10.1093/bioinformatics/btab877</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34983062">pmid:34983062</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8896603/">pmcid:PMC8896603</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jwsq66usmjgmndil22snpvdll4">fatcat:jwsq66usmjgmndil22snpvdll4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220222215912/https://watermark.silverchair.com/btab877.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAwMwggL_BgkqhkiG9w0BBwagggLwMIIC7AIBADCCAuUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMey9qZCND87VgMECSAgEQgIICtlOqzjgaTBJLhknGVddd-j5FxIt8_Mu_baMljXu2h84El7cit0WiGphR4D5cAlQdcx31cEqf4KBhYXlojvsLIrfGiLcazKVRsLZvBdcNojZG8-ropEVQwA-JNv9bPur5KbsOa1WrAen6F21JxH0zwoIhDQpl6sOcIEsV3uxuLBbXBDZMrXbSi_yA2mHnzGrGkBXVSqdA5ASNEVEWM_iFPecnUO9X5LAwp-K9mSng_eqIWgkBNl8WMPm3oeti04ALct0UbUGXTTiauGgpxqJHllEBLhJ1SBPHpXgXimg5JKmYMVEA34J9pltHW2com1dzGjcvGz3EKUpDGQ9kMhepWOc-_8r8h25iAYB2diJAuKf0L6wv-Ip1FypKaGqu8_an3aEGcSOqVneMU48ulDodXsDk7UZhwci8bv3H8I8fj4atwnyfz0swzIicy7qbdgwO27LOjxPIqqKX110IpEV0-0Immh5O_HmVuhve0-7VgjPdeSz4H0j4T8cFKxDeUjkc-NjVouLRFGelgz3R41JWbYcLiJXJiZPtDQP_RKPs33atVXMFZnmYB25IIqvMEdm3rELFQU1D_H1bW1n-TmZob1bCsvC6jYwx_76ft-0ENP-auiE_NYUN-6Rf_33gydu_-I0JzxC2A6Ez1LutE9SIkN7-z6VRen-7n_7icR42cEQN6jCR2NpBg2Mqh9ehSqXZOyK7TU-Y11afPLc9al9wS0OGjvKeH28GqOyPbIY0wtXnFDeyBNOymFWYKbK4w1ew--venSvjSLOtUI8hGaUtpShihlRRo2tEwnDm0QLYoStxvqKYoSpl8dP9iv2c-p6a4KtlIX7jXYIJ9tgtVg1v7ijYc4Z0akMsxEFQnIzDczInTAppi2DNYZvx90jOkr7JERhww6MUBE8D1JbwxXiNbkK9HI3W9m0" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4a/4a/4a4aab95cd45d8d383925dd39631524fbdfc14c4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btab877"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8896603" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

FLINO-A new method for immunofluorescence bioimage normalization

John Graf, Sanghee Cho, Elizabeth McDonough, Alex Corwin, Anup Sood, Andreas Lindner, Manuela Salvucci, Xanthi Stachtea, Sandra Van Schaeybroeck, Philip D Dunne, Pierre Laurent-Puig, Daniel Longley (+2 others)
<span title="2021-10-02">2021</span> <i title="Oxford University Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Multiplexed immunofluorescence bioimaging of single-cells and their spatial organization in tissue holds great promise to the development of future precision diagnostics and therapeutics.  ...  These methods were applied in both an unbiased grid object and segmented cell object workflow to 24 multiplexed biomarkers.  ...  Acknowledgements The authors wish to thank Chris Sevinsky, Yousef Al-Kofahi and Maria Zavodszky for the helpful technical discussions and feedback.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btab686">doi:10.1093/bioinformatics/btab686</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34601553">pmid:34601553</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8723144/">pmcid:PMC8723144</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vvpegndhmzgblh7taa33furkzi">fatcat:vvpegndhmzgblh7taa33furkzi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211006045706/https://watermark.silverchair.com/btab686.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAwEwggL9BgkqhkiG9w0BBwagggLuMIIC6gIBADCCAuMGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMTVR01OjK7MGk_nOTAgEQgIICtJTUv5xFtchZ76GGBdBRnS1p2nwoZCNpvWCIsXYqcUwGazDyvpI3KNU3PQe8BYEBY66lA_MPJ53DXW1ad-lYT2pdYiK0ZI98jOLoWetOuYoUIpyccPB9XQ--xNFcFsls4AWNnZffhz67MJYs3-TxLRUhBRME1aR0tNhJcNJIy71ss_YbnFt4P-TVdf8k6Jih4e3ZO7VGN7W38FNZZoUy9UlxaeK-cPhaPC5fyvl1gTD66UMJ-ulVYXeWnvbbtHxq8KB7eNwiq1Ir2erJGEizp6mKFXQFhHCqoOKkz5YOJ2InQiDkGy5aHuH_v7WJBMz77YEvHDSG7LviI7ZVgYs9VMABKlT4XpM66nYzIHu5COmYWPJZ_xnGjPEUPP-JlQ1Eg1XbuhgsQPLeWnVJhteAmKFbJt6m-pugAp7pfjIT03gkL-Kl9is7XSoUyJJv5pGFBGE3uatt7OVep6a1J2jr1Y51l7U_kxbXkahdOiV--eRIzB-87Xr2EeCVENqbtCRqKk7yXNThxQgm6-ifj-wI02bmUPNKVzefU9lcGQNBvvGqqoV5buTlPVdY-c7ENp8X4Hkxd4is_wCJtRbxF2tcqzsSDG2qddvnVgi7WScIsGorYb4QYWFUwuHPhzI62kb1FBAvNNlaV3VPgd4cb6X_J6OgINTnkcm5et7Dp4r21akkZL_XsJjYMfK_fcizv0HE4fdwCrHO9WVxleAagf8JK4jr4k7mE0sxRq9pqUU-thHLbZ1FBJtmMECeDoOJlFZEzXgukw9utZkNiLtGgYQCF3pZS10bkxszmgzYmHLTatz-JGc5pYHPzDXM4oJjwCTFaWJ8f7TYM_KEOnKZ6G4fYqWQC2zGKohuiO2M_RJQbbggbDexhm13NQrIz2nPqwtl_toTIhS0OyiNFmiWwBvS5djmVg9e" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6c/b4/6cb42e51d94338ba0fb7d25bc2e83ccb7af16f76.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btab686"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8723144" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Validation of multiplex immunofluorescence panels using multispectral microscopy for immune-profiling of formalin-fixed and paraffin-embedded human tumor tissues

Edwin R. Parra, Naohiro Uraoka, Mei Jiang, Pamela Cook, Don Gibbons, Marie-Andrée Forget, Chantale Bernatchez, Cara Haymaker, Ignacio I. Wistuba, Jaime Rodriguez-Canales
<span title="2017-10-17">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
Our goal was to validate multiplex immunofluorescence (mIF) panels to apply to formalin-fixed and paraffin-embedded tissues using a set of immune marker antibodies, with the Opal™ 7 color Kit (PerkinElmer  ...  After all primary antibodies were tested in positive and negative controls by immunohistochemistry and uniplex IF, panels were developed and simultaneous marker expressions were quantified using the Vectra  ...  In the multiplex IF slides, each batch was scanned with the Vectra imaging system using a tonsil as a control to calibrate the spectral image protocol.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-13942-8">doi:10.1038/s41598-017-13942-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29042640">pmid:29042640</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5645415/">pmcid:PMC5645415</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6axcmqejgbgtzmegxoxby5yore">fatcat:6axcmqejgbgtzmegxoxby5yore</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211170643/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5645415&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/92/a2/92a2598fe39bd261691ef3a1ebd15367cf3c1d64.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-13942-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5645415" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Society for Immunotherapy in Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation

Janis M Taube, Guray Akturk, Michael Angelo, Elizabeth L Engle, Sacha Gnjatic, Shirley Greenbaum, Noah F Greenwald, Cyrus V Hedvat, Travis J Hollmann, Jonathan Juco, Edwin R Parra, Marlon C Rebelatto (+15 others)
<span title="">2020</span> <i title="BMJ"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tcu4zb76ybaefkex5wp4pzcq3u" style="color: black;">Journal for ImmunoTherapy of Cancer</a> </i> &nbsp;
Multiplex immunohistochemistry (mIHC) and multiplex immunofluorescence (mIF) analyses are emerging technologies that can be used to help quantify immune cell subsets, their functional state, and their  ...  Quantitative image analysis of mIHC/mIF output and data management considerations will be addressed in a complementary manuscript from this task force.  ...  Additionally, the authors wish to thank the society for supporting the manuscript development.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/jitc-2019-000155">doi:10.1136/jitc-2019-000155</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32414858">pmid:32414858</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ytb3kt7iybafzaejm32v6du254">fatcat:ytb3kt7iybafzaejm32v6du254</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200709114107/https://jitc.bmj.com/content/jitc/8/1/e000155.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cc/52/cc529f33f1204b3c7a349a4e47160e45b0005426.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/jitc-2019-000155"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> bmj.org </button> </a>

A framework for multiplex imaging optimization and reproducible analysis [article]

Jennifer R Eng, Elmar Bucher, Zhi Hu, Ting Zheng, Summer Gibbs, Koei Chin, Joe W. Gray
<span title="2021-11-30">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
normalization of the multiplex imaging with a focus on cyclic immunofluorescence (CyCIF).  ...  We developed a python software, jinxif, for reproducible image processing and utilize Jupyter notebooks to share our optimization of signal removal, antibody specificity, background correction and batch  ...  Acknowledgments We would like to thank former lab members Aesoon Bensen and Lydia Grace Campbell as well as former interns Clayton Peltz and Cole Meyer for assistance with staining and imaging.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.11.29.470281">doi:10.1101/2021.11.29.470281</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/twr7ftnotfgfxaqofmsqto5eti">fatcat:twr7ftnotfgfxaqofmsqto5eti</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220201055359/https://www.biorxiv.org/content/biorxiv/early/2021/11/30/2021.11.29.470281.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f2/21/f2219cb2f0d1365c5157f7ede58b49063f389727.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.11.29.470281"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Front Matter: Volume 10581

Metin N. Gurcan, John E. Tomaszewski
<span title="2018-06-01">2018</span> <i title="SPIE"> Medical Imaging 2018: Digital Pathology </i> &nbsp;
Utilization of CIDs allows articles to be fully citable as soon as they are published online, and connects the same identifier to all online and print versions of the publication.  ...  Publication of record for individual papers is online in the SPIE Digital Library. SPIEDigitalLibrary.org Paper Numbering: Proceedings of SPIE follow an e-First publication model.  ...  We would like to acknowledge the excellent work in the following papers:  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1117/12.2323941">doi:10.1117/12.2323941</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wyt7wxgl4nebxooizvt2efswwq">fatcat:wyt7wxgl4nebxooizvt2efswwq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427040233/https://www.spiedigitallibrary.org/conference-proceedings-of-spie/10581/1058101/Front-Matter-Volume-10581/10.1117/12.2323941.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f2/f7/f2f78f94cbb87ea213b65e4637295b7ffeb85541.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1117/12.2323941"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Procedural Requirements and Recommendations for Multiplex Immunofluorescence Tyramide Signal Amplification Assays to Support Translational Oncology Studies

Parra, Jiang, Solis, Mino, Laberiano, Hernandez, Gite, Verma, Tetzlaff, Haymaker, Tamegnon, Rodriguez-Canales (+3 others)
<span title="2020-01-21">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2zwku6u6nfdcri773tpisi6ldi" style="color: black;">Cancers</a> </i> &nbsp;
In the development of a multiplex immunofluorescence (IF) platform and the optimization and validation of new multiplex IF panels using a tyramide signal amplification system, several technical requirements  ...  Our laboratory has stained approximately 4000 formalin-fixed, paraffin-embedded tumor samples using the multiplex IF TSA system for immune profiling of several labeled biomarkers in a single slide to elucidate  ...  Spectral Library In parallel to antibody optimization, creation of a spectral library is necessary to detect the correct spectra excitation from each fluorophore in the multiplex IF-stained slide and avoid  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers12020255">doi:10.3390/cancers12020255</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31972974">pmid:31972974</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7072187/">pmcid:PMC7072187</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cxioy7meprdmnnlt3z5jocodl4">fatcat:cxioy7meprdmnnlt3z5jocodl4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200212095916/https://res.mdpi.com/d_attachment/cancers/cancers-12-00255/article_deploy/cancers-12-00255.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d3/b0/d3b0a2c47e74a5a80e4b43e02521c3684baee794.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers12020255"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7072187" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Spatial proximity between T and PD-L1 expressing cells as a prognostic biomarker for oropharyngeal squamous cell carcinoma

Anna Maria Tsakiroglou, Martin Fergie, Ken Oguejiofor, Kim Linton, David Thomson, Peter L. Stern, Susan Astley, Richard Byers, Catharine M. L. West
<span title="2019-12-06">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/k7cos7qqgzazliffoxrrx3awka" style="color: black;">British Journal of Cancer</a> </i> &nbsp;
The HID method can quantify spatial interactions considered to reflect immune escape and generate prognostic information in OPSCC.  ...  We tested a new automatic approach to select tissue and quantify the frequencies of cell-cell spatial interactions occurring in the PD1/PD-L1 pathway, hypothesised to reflect immune escape in oropharyngeal  ...  Multiplex staining and multispectral scanning Multiplex immunofluorescent staining was performed using the Ventana auto-staining platform (Ventana Medical Systems, Oro Valley, Arizona, United States) and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41416-019-0634-z">doi:10.1038/s41416-019-0634-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31806878">pmid:31806878</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7028988/">pmcid:PMC7028988</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vagcws4oizgobkuxmruwn7ynwq">fatcat:vagcws4oizgobkuxmruwn7ynwq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428110339/https://www.nature.com/articles/s41416-019-0634-z.pdf?error=cookies_not_supported&amp;code=d5ea0394-fbed-4139-a167-19fbcdb5789a" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0a/de/0adecb9c296ec40bb4551c5ee4267eea33959b0f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41416-019-0634-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7028988" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cell-based quantification of molecular biomarkers in histopathology specimens

Yousef Al-Kofahi, Wiem Lassoued, Kedar Grama, Sumit K Nath, Jianliang Zhu, Ridha Oueslati, Michael Feldman, William M F Lee, Badrinath Roysam
<span title="">2011</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uxv6qrdvtngyfnxtwbqkjbbbgi" style="color: black;">Histopathology</a> </i> &nbsp;
Methods and results-Tissue specimens were multiplex-immunostained to reveal cell structures, cell type markers, and analytes, and imaged with multispectral microscopy.  ...  The image data were processed with novel software that automatically delineates and types each cell in the field, measures morphological features, and quantifies analytes in different subcellular compartments  ...  The authors thank Dr Cliff Hoyt (CRi, Woburn, MA, USA) for helpful discussions, and the staff at CRi Inc. for technical assistance.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1365-2559.2011.03878.x">doi:10.1111/j.1365-2559.2011.03878.x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21771025">pmid:21771025</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3142095/">pmcid:PMC3142095</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6ypdqxab7nctzbs7pe5neq6u7i">fatcat:6ypdqxab7nctzbs7pe5neq6u7i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206162803/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3142095&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f1/4f/f14fa9e857837ec58114ef778f31edabbc755809.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1365-2559.2011.03878.x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142095" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A robust multiplex immunofluorescence and digital pathology workflow for the characterisation of the tumour immune microenvironment

Amélie Viratham Pulsawatdi, Stephanie G. Craig, Victoria Bingham, Kris McCombe, Matthew P. Humphries, Seedevi Senevirathne, Susan D. Richman, Phil Quirke, Leticia Campo, Enric Domingo, Timothy S. Maughan, Jacqueline A. James (+1 others)
<span title="2020-07-16">2020</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wilcjb4re5hs5egpxpnhcm4lj4" style="color: black;">Molecular Oncology</a> </i> &nbsp;
In this study, we aimed to validate a multiplex immunofluorescence workflow in two complementary multiplex panels and evaluate the tumour immune microenvironment in colorectal cancer formalin-fixed paraffin-embedded  ...  Overall, we report the optimisation and validation of a multiplex immunofluorescence process, from staining to image analysis, ensuring assay robustness.  ...  Natural variation in tissue thickness is expected and often seen in routine basic and special stains due to manual sectioning of the tissue.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/1878-0261.12764">doi:10.1002/1878-0261.12764</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32671911">pmid:32671911</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o2nmojii7ra5fm4ryk4gtjzb7u">fatcat:o2nmojii7ra5fm4ryk4gtjzb7u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201104095530/https://pureadmin.qub.ac.uk/ws/files/216003363/Character.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/93/c2/93c2a3d9426eee9d058b9ef5d2b050218380f253.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/1878-0261.12764"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a>

Prediction of radio-responsiveness with immune-profiling in patients with rectal cancer

In Ja Park, Soyeon An, Sang-Yeob Kim, Hye Min Lim, Seung-Mo Hong, Mi-Ju Kim, Yun Jae Kim, Chang Sik Yu
<span title="2017-07-25">2017</span> <i title="Impact Journals, LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yubgl6cdcrekxpjzhshpw23l3i" style="color: black;">OncoTarget</a> </i> &nbsp;
Multispectral imaging and digital analysis to visualize and quantify specific immune infiltrates were performed using the Vectra imaging system (Perkin-Elmer).  ...  We evaluate whether the tumor immune infiltrate (TIL) could be used for prediction of responsiveness to preoperative chemoradiotherapy (PCRT) in rectal cancers.  ...  Pretreatment biopsy slides were reviewed by a pathologist (SMH) and one representative slide was selected for multiplexed immunofluorescence. Informed consent was waived.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.19558">doi:10.18632/oncotarget.19558</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29108360">pmid:29108360</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5668093/">pmcid:PMC5668093</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7bv7or7dsfbcpgmhqpgzqktyha">fatcat:7bv7or7dsfbcpgmhqpgzqktyha</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720042052/http://www.oncotarget.com/index.php?journal=oncotarget&amp;page=article&amp;op=download&amp;path%5B%5D=19558&amp;path%5B%5D=62502" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/35/8f/358f74b5995cb098a12a7a278ef848dd8906636d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.19558"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668093" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Working with Commercially Available Quantum Dots for Immunofluorescence on Tissue Sections

Sandrine Prost, Ria E. B. Kishen, David C. Kluth, Christopher O. C. Bellamy, Makoto Kanzaki
<span title="2016-09-29">2016</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
We present here our investigation of the stability of original and Vivid Qdots in solution and in immunohistochemistry, highlight the potential pitfalls and propose a protocol for stable and reliable multiplex  ...  For many years quantum dot conjugated products have been available in multiple forms for fluorescence imaging of tissue sections under the trademark name Qdot®.  ...  Acknowledgments The work was supported by a project grant from the CSO (Chief Scientist Office Scotland, http://www.cso.scot.nhs.uk/) ETM/189 to DK, CB, and SP, a Moray Endowment Fund award to SP (University  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0163856">doi:10.1371/journal.pone.0163856</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27685858">pmid:27685858</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5042461/">pmcid:PMC5042461</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u4rg3pktaffp7gk35m4jall574">fatcat:u4rg3pktaffp7gk35m4jall574</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171012023426/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0163856&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/67/99/679938e62260dc3ecbd7075c6d6b7baf5fe35db6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0163856"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042461" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Multiplexed Immunohistochemistry for Molecular and Immune Profiling in Lung Cancer—Just About Ready for Prime-Time?

Paul Hofman, Cécile Badoual, Fiona Henderson, Léa Berland, Marame Hamila, Elodie Long-Mira, Sandra Lassalle, Hélène Roussel, Véronique Hofman, Eric Tartour, Marius Ilié
<span title="2019-02-27">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2zwku6u6nfdcri773tpisi6ldi" style="color: black;">Cancers</a> </i> &nbsp;
Multiplexed immunohistochemistry is an effective and proficient approach to simultaneously identify specific proteins or molecular abnormalities, to determine the spatial distribution and activation state  ...  This review provides views on the current technological status and evidence for clinical applications of multiplexing and how it could be applied to optimize clinical management of patients with lung cancer  ...  Immunofluorescent Multiplexing Localization of Immune Cells and Their Relationships with Immunosuppressive Markers in the Tumor Microenvironment The multiplex immunofluorescence techniques better distinguish  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers11030283">doi:10.3390/cancers11030283</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30818873">pmid:30818873</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6468415/">pmcid:PMC6468415</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jkf4jkxcybejzk4ohhe3qnqf5a">fatcat:jkf4jkxcybejzk4ohhe3qnqf5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190505205915/https://res.mdpi.com/cancers/cancers-11-00283/article_deploy/cancers-11-00283.pdf?filename=&amp;attachment=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/40/9a/409afce1ea82a6ddf56f643a2f554fe75f151498.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers11030283"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6468415" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Easy Employment and Crosstalk-Free Detection of Seven Fluorophores in a Widefield Fluorescence Microscope

Sebastian Bhakdi, Ponpan Thaicharoen
<span title="2018-06-01">2018</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/26pa4o55qbcudfcimiw32nr32y" style="color: black;">Methods and Protocols</a> </i> &nbsp;
Immunofluorescence staining has become an essential tool in pathology and biomedical sciences to identify rare cells, cell-cell interactions, and submicroscopic cellular components.  ...  Quantification of crosstalk between channels and actual seven-color imaging of cancer cells spiked into leukocytes demonstrate that there is no need for digital compensation correction algorithms.  ...  to Ema Naito and Sebastian Grote for language editing of the manuscript; and to Scott Phillips from Chroma Technology for kindly permitting us to use the Chroma Spectra Viewer.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/mps1020020">doi:10.3390/mps1020020</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31164563">pmid:31164563</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6526416/">pmcid:PMC6526416</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oh4fln72wvbyjkzhcv5xhyulyq">fatcat:oh4fln72wvbyjkzhcv5xhyulyq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728062647/https://res.mdpi.com/def5020008c7839fd08b6d2c2ccbb13d11ee5d56f5b44606a87a2e525653c21790a14eb64a942c01d0835114fc4d5ccca16f4bd2479d0b5fb5dac6d873d89885e9d61532c7a0053136fe89e236af4293c07f698d25dbc094252460d47bc66f166837dece516ce256aef8128741ebf38734d1c8ed1d55da7c15f69be78a0e5cc9c4924c96af4b3b?filename=&amp;attachment=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/db/c7/dbc75a1b244cedd30b1f485aee32791ccf822f5e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/mps1020020"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526416" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cell and Tissue Display

Nicholas Theodosakis, Goran Micevic, Marcus W. Bosenberg, Nemanja Rodić
<span title="2016-06-07">2016</span> <i title="SAGE Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rpioyarmz5fgjmeoodpqcal34a" style="color: black;">Journal of Histochemistry and Cytochemistry</a> </i> &nbsp;
; and the generation of control slides for laboratory proficiency testing.  ...  We developed a method, termed Cell and Tissue Display (CTD), for embedding 16 or more different tissue samples in multicompartment agarose blocks.  ...  Ruth Halaban and Antonietta Bacchiocchi for providing the human melanoma cell lines used to validate this technique. We also thank Mrs. Nancy Troiano, of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1369/0022155416651065">doi:10.1369/0022155416651065</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27270967">pmid:27270967</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4931762/">pmcid:PMC4931762</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zno5nttfq5d3zpj344sizp37iy">fatcat:zno5nttfq5d3zpj344sizp37iy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200207200601/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4931762&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/04/07/04072b0c8a71f64d2a394a4201a39f5356e1bea1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1369/0022155416651065"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4931762" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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