Josef Špidlen

Becton Dickinson (United States) — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

17h-index4.1kcitations48works1.22yr avg
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Research Topics

Single-cell and spatial transcriptomics(34), Cell Image Analysis Techniques(23), Gene expression and cancer classification(17), Electronic Health Records Systems(5), Advanced Fluorescence Microscopy Techniques(5)

Publications46 total

Response to “Bridging the implementation gap in <scp>AI</scp> ‐assisted flow cytometry”
Cytometry Part B Clinical Cytometry·2026
Current and Future Challenges in Cytometry: Reports of the CYTO 2025 Conference Workshops
Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)·2026Open Access
Cyt‐Geist: Current and Future Challenges in Cytometry: Reports of the <scp>CYTO</scp> 2025 Conference Workshops
Cytometry Part A·2025Open Access
<scp>AI</scp> in flow cytometry: Current applications and future directions
Cytometry Part B Clinical Cytometry·2025· 3 cited
<scp>SingletSeeker</scp>: An unsupervised clustering approach for automated singlet discrimination in cytometry
Cytometry Part B Clinical Cytometry·2024· 3 citedOpen Access
AutoSpill is a principled framework that simplifies the analysis of multichromatic flow cytometry data
Nature Communications·2021· 52 citedOpen Access
Data File Standard for Flow Cytometry, Version <scp>FCS</scp> 3.2
Cytometry Part A·2020· 13 cited
<scp>ISAC</scp> Probe Tag Dictionary: Standardized Nomenclature for Detection and Visualization Labels Used in Cytometry and Microscopy Imaging
Cytometry Part A·2020· 3 citedOpen Access
AutoSpill: A method for calculating spillover coefficients to compensate or unmix high-parameter flow cytometry data
2020· 4 citedOpen Access
Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets
Nature Communications·2019· 591 citedOpen Access
20,000 layers under the model: Bayesian neural networks improve the robustness of human PBMC classifications using immunologist encoded bias
The Journal of Immunology·2019
Automated optimized parameters for t-distributed stochastic neighbor embedding improve visualization and allow analysis of large datasets
2018· 14 citedOpen Access
Methodology for evaluating and comparing flow cytometers: A multisite study of 23 instruments
Cytometry Part A·2018· 21 citedOpen Access
Evaluating flow cytometer performance with weighted quadratic least squares analysis of L<scp>ED</scp> and multi‐level bead data
Cytometry Part A·2017· 21 citedOpen Access
Use FlowRepository to share your clinical data upon study publication
Cytometry Part B Clinical Cytometry·2016· 13 citedOpen Access
flow<scp>C</scp>lean: Automated identification and removal of fluorescence anomalies in flow cytometry data
Cytometry Part A·2016· 66 citedOpen Access
<scp>ISAC</scp>'s <scp>G</scp>ating‐<scp>ML</scp> 2.0 data exchange standard for gating description
Cytometry Part A·2015· 18 citedOpen Access
ISAC's classification results file format
Cytometry Part A·2014· 4 citedOpen Access
Flow Cytometry Bioinformatics
PLoS Computational Biology·2013· 103 citedOpen Access
GenePattern flow cytometry suite
Source Code for Biology and Medicine·2013· 17 citedOpen Access
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Frequent Co-authors

Ryan R. Brinkman(27), Wayne Moore(8), Robert C. Leif(7), Petr Hanzlíček(7), Jana Zvárová(6), Richard Halpert(5), James C. S. Wood(5), Richard H. Scheuermann(5), David R. Parks(5), Christopher O. Ciccolella(4), Michael Goldberg(4), Qian Yu(4), Peter Wilkinson(4), Karin Breuer(4), Chris Bray(4), Goce Bogdanoski(4), Nolwenn Le Meur(3), Robert Gentleman(3), Adam Treister(3), Mario Roederer(3)