tSNE Platform Improvements

  • Increased speed by 3x.
  • Decreased memory requirements.
    (Together, these two improvements allow tSNE to be run on one million events with 12 parameters! Note that this can take two hours on a laptop.)
  • Can initialize the tSNE algorithm with previously-computed LDA parameters.
  • Can also initialize from previously-added PCA parameters—this means you can compute PCA on a predicate sample, copy the PCA vectors to other samples, and initialize SNEe on those identically-computed vectors for greater cross-sample similarity.


  • v9.9 no longer shows uncompensated parameters in menus by default (unless you hold down option key). But when you concatenated files and add a keyword as a new parameter, it assumed this was an uncompensated parameter and didn’t show it. New concatenated files add a notation that this parameter should be shown in menus.


  • Spectral compensation UI: Minor updates.

Layout Editor

  • New “Polychromatic Y by Y” creator in the Layout Editor. Access is similar to the Y by Y platform (select a single graphic and choose Y by Y from the menu or the contextual menu). Select parameters—FlowJo will create a copy of the selected plot with every pair of the selected parameters controlling color in a polychromatic plot. (This tool is useful for exploring a tSNE plot for expression and co-expression of markers—a single click to get tons of info.)
  • Removed limit of 50 overlays in a single Layout graph item.
  • Fix: Reducing dimensions of an LE table containing objects doesn’t crash.
  • Fix: Copying or pasting a textbox in the Layout Editor preserves all styling information.

Misc. Fixes

  • Fix (table outputs): Reduce double commas in gate names to one.
  • Fix: Minor UI bugs in the custom transformation editor dialog.
  • Implement smart sorting of groups, tables, and layouts in menus and lists.
  • Fix: Prevent crash if PCA platform shows only one parameter.

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