Performance metric of OpenCyto on the flow cytometry and CyTOF data sets, on a single-processor machine with 8 GB of RAM.

OpenCyto can reproduce the FlowJo manual gates from a 16-workspace data set in 21 minutes with a peak memory usage of 1.8 GB. Once gated, the data occupies only 4.6 MB of RAM and is efficiently stored on disk in the HDF5/NetCDF format. Automated gating of the same data set using on OpenCyto GatingTemplate to generate data-driven gates for each of the 470 samples takes 1.74 hours on a single-processor. This can be parallelized across multiple cores for greater efficiency. The 420×24 Boolean subsets of 4-cytokine producing cells can be generated and extracted efficiently, taking only 17 minutes for 7520 different subsets. Analogous results are shown for the CyTOF data, which has higher dimensionality. Calculating the Boolean subsets of 9 cytokine gates for the four maturation subsets in the data was extremely quick. In contrast, the 4×29 Boolean subsets took 104 minutes to compute in FlowJo.
Performance metric of OpenCyto on the flow cytometry and CyTOF data sets, on a single-processor machine with 8 GB of RAM.