Critical assessment of automated flow cytometry data analysis techniques

Nima Aghaeepour, Greg Finak, Holger Hoos, Tim R. Mosmann, Ryan Brinkman, Raphael Gottardo, Richard H. Scheuermann, David Dougall, Alireza Hadj Khodabakhshi, Phillip Mah, Gerlinde Obermoser, Josef Spidlen, Ian Taylor, Sherry A. Wuensch, Jonathan Bramson, Connie Eaves, Andrew P. Weng, Edgardo S. Fortuno, Kevin Ho, Tobias R. KollmannWade Rogers, Stephen De Rosa, Bakul Dalai, Ariful Azad, Alex Pothen, Aaron Brandes, Hannes Bretschneider, Robert Bruggner, Rachel Finck, Robin Jia, Noah Zimmerman, Michael Linderman, David Dill, Gary Nolan, Cliburn Chan, Faysal El Khettabi, Kieran O'Neill, Maria Chikina, Yongchao Ge, Stuart Sealfon, István Sugár, Arvind Gupta, Parisa Shooshtari, Habil Zare, Philip L. De Jager, Mike Jiang, Jens Keilwagen, Jose M. Maisog, George Luta, Andrea A. Barbo, Peter Májek, Jozef Vilček, Tapio Manninen, Heikki Huttunen, Pekka Ruusuvuori, Matti Nykter, Geoffrey J. McLachlan, Kui Wang, Iftekhar Naim, Gaurav Sharma, Radina Nikolic, Saumyadipta Pyne, Yu Qian, Peng Qiu, John Quinn, Andrew Roth, Pablo Meyer, Gustavo Stolovitzky, Julio Saez-Rodriguez, Raquel Norel, Madhuchhanda Bhattacharjee, Michael Biehl, Philipp Bucher, Kerstin Bunte, Barbara Di Camillo, Francesco Sambo, Tiziana Sanavia, Emanuele Trifoglio, Gianna Toffolo, S. D. Slavica Dimitrieva, Rene Dreos, Giovanna Ambrosini, Jan Grau, Ivo Grosse, Stefan Posch, Nicolas Guex, Miron Kursa, Witold Rudnicki, Bo Liu, Mark Maienschein-Cline, Petra Schneider, Michael Seifert, Marc Strickert, Jose M.G. Vilar

Research output: Contribution to journalArticlepeer-review

419 Scopus citations


Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) challenges were established to compare the performance of these methods on two tasks: (i) mammalian cell population identification, to determine whether automated algorithms can reproduce expert manual gating and (ii) sample classification, to determine whether analysis pipelines can identify characteristics that correlate with external variables (such as clinical outcome). This analysis presents the results of the first FlowCAP challenges. Several methods performed well as compared to manual gating or external variables using statistical performance measures, which suggests that automated methods have reached a sufficient level of maturity and accuracy for reliable use in FCM data analysis.

Original languageEnglish (US)
Pages (from-to)228-238
Number of pages11
JournalNature Methods
Issue number3
StatePublished - Mar 2013
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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