Cytometry - compensation, gating, and the readable workspace

1 · Learn the move · Template pattern

PARALLEL TRACK - complete this one only if pl1 pointed you here. Flow cytometry hides its record in plain sight: an FCS file's text segment - parameters, voltages, acquisition context - reads as plain text and almost nobody looks; the data segment does not read at all - that is what flowCore, FlowKit, or fcsparser are for. Your FlowJo .wsp is XML: a legible record of every gate a human drew. The template pattern turns this into discipline: a fixed gating-record template - population, parent, channels, gate coordinates or method, compensation source, event counts in and out - extracted from the .wsp rather than transcribed from memory. Fill it twice and gate drift becomes a diff instead of an argument. The non-negotiable: compensation. Uncompensated data gates cheerfully into nonsense, so the spillover matrix travels with every analysis - no exceptions.

Author my cytometry record pipeline: (1) a script using [fcsparser/FlowKit] that extracts from each .fcs the parameter list, $PnN/$PnS names, event count, and the spillover matrix from the text segment; (2) a .wsp parser that fills my gating-record template per population: POPULATION / PARENT / CHANNELS / GATE METHOD+COORDS / COMP SOURCE / EVENTS IN -> OUT / PERCENT OF PARENT; (3) a drift check that diffs two experiments' filled templates gate by gate, flagging coordinate shifts beyond [tolerance]; (4) a hard stop with a named error if any sample lacks a spillover matrix. Anything not in the files = [NEEDS: ...], never reconstructed from what my panel usually looks like.