Publications by authors named "Josef Spidlen"

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Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2025 Conference Workshops.
Paul K Wallace, Evan R Jellison, Sherry Thornton, Kathleen Kluepfel, Jessica Back, Josef Spidlen

Cytometry A· December 2025

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SingletSeeker: An unsupervised clustering approach for automated singlet discrimination in cytometry.
Mark Colasurdo, Laura Ferrer-Font, Aaron Middlebrook, Andrew J Konecny, Martin Prlic, Josef Spidlen

Cytometry B Clin Cytom· September 2025

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AI in flow cytometry: Current applications and future directions.
Alice Yue, Ryan R Brinkman, Veronica Nash, Fabian Junker, Goce Bogdanoski, Josef Spidlen

Cytometry B Clin Cytom· September 2025

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AutoSpill is a principled framework that simplifies the analysis of multichromatic flow cytometry data.
Carlos P Roca, Oliver T Burton, Václav Gergelits, Teresa Prezzemolo, Carly E Whyte, Josef Spidlen

Nat Commun· May 2021

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ISAC Probe Tag Dictionary: Standardized Nomenclature for Detection and Visualization Labels Used in Cytometry and Microscopy Imaging.
Kim R M Blenman, Josef Spidlen, David R Parks, Wayne Moore, Adam Treister

Cytometry A· January 2021

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Data File Standard for Flow Cytometry, Version FCS 3.2.
Josef Spidlen, Wayne Moore, David Parks, Michael Goldberg, Kim Blenman

Cytometry A· January 2021

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Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets.
Anna C Belkina, Christopher O Ciccolella, Rina Anno, Richard Halpert, Josef Spidlen

Nat Commun· November 2019

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Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition).
Andrea Cossarizza, Hyun-Dong Chang, Andreas Radbruch, Andreas Acs, Dieter Adam, Josef Spidlen

Eur J Immunol· October 2019

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Methodology for evaluating and comparing flow cytometers: A multisite study of 23 instruments.
David R Parks, Wayne A Moore, Ryan R Brinkman, Yong Chen, Danilo Condello, Josef Spidlen

Cytometry A· November 2018

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Use FlowRepository to share your clinical data upon study publication.
Josef Spidlen, Ryan R Brinkman

Cytometry B Clin Cytom· January 2018

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Guidelines for the use of flow cytometry and cell sorting in immunological studies.
Andrea Cossarizza, Hyun-Dong Chang, Andreas Radbruch, Mübeccel Akdis, Immanuel Andrä, Josef Spidlen

Eur J Immunol· October 2017

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Evaluating flow cytometer performance with weighted quadratic least squares analysis of LED and multi-level bead data.
David R Parks, Faysal El Khettabi, Eric Chase, Robert A Hoffman, Stephen P Perfetto, Josef Spidlen

Cytometry A· March 2017

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flowClean: Automated identification and removal of fluorescence anomalies in flow cytometry data.
Kipper Fletez-Brant, Josef Špidlen, Ryan R Brinkman, Mario Roederer, Pratip K Chattopadhyay

Cytometry A· May 2016

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ISAC's Gating-ML 2.0 data exchange standard for gating description.
Josef Spidlen, Wayne Moore, , Ryan R Brinkman

Cytometry A· July 2015

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ISAC's classification results file format.
Josef Spidlen, Chris Bray, , Ryan R Brinkman

Cytometry A· January 2015

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Flow cytometry bioinformatics.
Kieran O'Neill, Nima Aghaeepour, Josef Spidlen, Ryan Brinkman

PLoS Comput Biol· August 2014

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GenePattern flow cytometry suite.
Josef Spidlen, Aaron Barsky, Karin Breuer, Peter Carr, Marc-Danie Nazaire

Source Code Biol Med· July 2013

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ICEFormat-the image cytometry experiment format.
Josef Spidlen, David Novo

Cytometry A· December 2012

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FlowRepository: a resource of annotated flow cytometry datasets associated with peer-reviewed publications.
Josef Spidlen, Karin Breuer, Chad Rosenberg, Nikesh Kotecha, Ryan R Brinkman

Cytometry A· September 2012

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Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) compliant manuscript using the International Society for Advancement of Cytometry (ISAC) FCS file repository (FlowRepository.org).
Josef Spidlen, Karin Breuer, Ryan Brinkman

Curr Protoc Cytom· July 2012

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FCS 3.1 Implementation guidance.
Chris Bray, Josef Spidlen, Ryan R Brinkman

Cytometry A· June 2012

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Flow cytometry data standards.
Josef Spidlen, Parisa Shooshtari, Tobias R Kollmann, Ryan R Brinkman

BMC Res Notes· March 2011

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Data File Standard for Flow Cytometry, version FCS 3.1.
Josef Spidlen, Wayne Moore, David Parks, Michael Goldberg, Chris Bray

Cytometry A· January 2010

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FuGEFlow: data model and markup language for flow cytometry.
Yu Qian, Olga Tchuvatkina, Josef Spidlen, Peter Wilkinson, Maura Gasparetto

BMC Bioinformatics· June 2009

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flowCore: a Bioconductor package for high throughput flow cytometry.
Florian Hahne, Nolwenn LeMeur, Ryan R Brinkman, Byron Ellis, Perry Haaland, Josef Spidlen

BMC Bioinformatics· April 2009

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