The FlowRepository admin email ( has not been working since December 13th 2018 and is still not working. From January 3rd 2019 the website will now link directly to the admin, Justin, through his email of If you had sent a support ticket or any other means to connect to the admins of FlowRepository between those two dates, those emails did not go through. Please forward any emails to him, or re-create any issues through the website. Sorry for any inconvenience and thank you for your patience and understanding.


Experiment Overview

Repository ID: FR-FCM-ZZPH Experiment name: Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry (CyTOF) data MIFlowCyt score: 31.25%
Primary researcher: Lukas Weber PI/manager: Lukas Weber Uploaded by: Lukas Weber
Experiment dates: 2015-09-01 - Dataset uploaded: Feb 2016 Last updated: Dec 2016
Keywords: None Manuscripts: [27992111]
Organizations: University of Zurich, Institute of Molecular Life Sciences, Mark Robinson lab, Zurich, (Switzerland)
Purpose: This repository contains pre-processed data files to reproduce the analyses in our paper on comparing clustering methods for high-dimensional flow and mass cytometry (CyTOF) data. There are 6 main data sets, and 2 data sets from the FlowCAP-I challenges, as described in the paper. R scripts to reproduce all analyses and figures in the paper (including scripts to prepare the data files) are available from GitHub at: The final paper is published in Cytometry Part A, 89A: 1084-1096, available open access at:
Conclusion: None
Comments: For each of the 6 main data sets, there is one main .fcs file, plus an additional .fcs file labeled "notransform". The "notransform" files contain non-transformed data, where the standard arcsinh transform has not yet been applied. For the two FlowCAP data sets, non-transformed data is not available. Manually gated population labels are included as a column within the .fcs files. The "population_names" .txt files (attachments) provide meta-data of cell population names corresponding to each label (for the data sets with multiple populations of interest; see paper). Gating-ML 2.0 .xml files (attachments) provide the gating schemes for data sets Nilsson_rare and Mosmann_rare.
Funding: Not disclosed
Quality control: None
Download FCS Files or login and see the dataset in your inbox for further annotation details.