inForm FlowJo tSNE

A.
Retains spatial information + ± -
Visualization of extra parameters - + ±
Reproducibility of analysis + + -
Customization of analysis output - + +
Automatic detection/adjustment of scales - - +
Ability to share/distribute analysis workspace - + ±
Allows “gating” of structures - + ±
Allows combinatorial/exclusive phenotyping - + ±
Direct comparison of cellular populations - + ±
The generation of confidence values + - -
Quantify differences in cellular expression - + ±
Ease of editing gating/categories - + ±
Unsupervised/empirical Empirical Empirical Unsupervised
Manual/automated Mixed Manual Automated
Analysis time ~8 hours ~5 hours ~3 hours
Learning curve for beginners Mid Low Mid
Price of analysis (licenses) $$$ $ $$
Data input .im3 file Converted .FCS file Converted .FCS file

B.
Manual Counting inForm FlowJo tSNE
2817 DAPI+ events 2825 DAPI+ events 2827 DAPI+ events 1852 DAPI+ events
CD4 T cells CD4 T cells CD4 T cells
CD4 T cells
T regs FoxP3+ T regs
CD8 T cells
CD8 T cells CD8 T cells CD8 T cells
B cells
B cells B cells B cells
Macrophages
Macrophages Macrophages Macrophages
Other
Other Other Other

% of events, WT #1

C. Analysis Method
Manual Counting inForm FlowJo tSNE
CD4 T cells 11.40% 10.60% 22.57% 11.00%
T regs 0.39% 0.92% 0.85% ND
Cell Type

CD8 T cells 17.86% 11.90% 13.41% 9.67%

B cells 5.89% 6.41% 5.97% 5.18%
Macrophages 2.06% 3.12% 3.64% 3.08%
Other 62.41% 67.08% 53.56% 71.07%