One acquisition in. A straight answer on whether it can be gated.
Paste the FCS keyword block — or drop the .fcs file itself, it is read in
your browser and never uploaded. The page decodes the HEADER and TEXT segments, builds the
channel table from $PnN, $PnS, $PnB, $PnE
and $PnR, derives the event rate from $TOT and the clock keywords,
and checks the parameter block against itself.
Both examples ship with a saved model run for all three lanes, so you can see the whole
answer — including the methods prose — without signing in and without spending a
credit.
Working
lane
posture
confidence
cytometer
findings
worst
blocking
Findings
id
sev
area
target
title
blocks
keywords cited
Parameters, graded
Every parameter in the file, including scatter and time. A channel
with nothing wrong is graded ok with a note on what it is for — an
omitted channel would be indistinguishable from a channel the answer never read.
n
name
marker
role
grade
issue
what it can be used for
Spillover pairs
Every pair at or above 5% of the donor dye's signal, plus any
negative coefficient. The percentages are the ones in your matrix — a number that is
not is reported in the grounding audit above.
id
from
into
coefficient
sev
Markers
One row per panel row, plus every labelled fluorescence detector
that had no panel row. The reasoning is stain index: antigen density times fluorochrome
brightness, against the spillover the detector receives.
marker
fluorochrome
detector
verdict
why
Controls
What would settle each open question, and what happens without it.
control
settles
status
note
Methods sections
Prose, in publication register. Anything the file does not carry is
written as a bracketed lookup rather than invented, so a placeholder in this text is a
deliberate instruction to go and find the value.
Reporting checklist
Each minimum-information item, and whether this file states it,
states it partially, or cannot state it at all. An item marked stated whose
keyword is absent from your file is contradicted in the grounding audit.
item
status
where it comes from
Artifacts
Documents, not commands. Nothing here is executed by this page and
nothing here tells you to run anything — they are the audit, the review and the methods
text as files you can put in a lab record or a manuscript.
Prescan reconciliation
Every deterministic flag the browser raised, and what the run did with
it. A flag deliberately set aside with a reason is a correct answer; a flag the run never
mentions is not.
Assumptions and open questions
Next steps
Summary
Raw model reply
The reply did not parse as the structured answer, so it is shown as it arrived.
Your recent reviews
If that did not work
Check that the prescan says it read something — the stat line next to the paste box
counts keywords, parameters, panel rows and matrix size. Check that you are signed in, and
that your balance covers the reservation next to the run button. Both bundled examples always
work and cost nothing, so they are the quickest way to tell a problem with your paste apart
from a problem with the service.
What this does, and what it does not
The prescan is parsing and arithmetic, not opinion. When it decodes a dropped file it reads
the 58-byte HEADER for the version string and the six segment offsets, then splits the TEXT
segment on its own first byte, treating a doubled delimiter as an escaped literal —
which is why a marker name containing the delimiter survives. The DATA segment is never
touched, so a 400 MB acquisition costs a few kilobytes of work and the file never leaves your
browser.
When it reports a condition number it has inverted your spillover matrix by Gauss-Jordan
elimination with partial pivoting and multiplied the infinity norms of the matrix and its
inverse. That number is not decoration: compensation multiplies every event by that inverse,
so a condition number of 40 means the one percent error a good single-stain control leaves in
a coefficient can arrive as a forty percent error in a compensated value. A singular matrix
has no inverse at all, which means two detectors have been described as seeing
indistinguishable mixtures and no arithmetic separates them.
When it says a population is out of reach it has done the Poisson arithmetic. At 8,000
recorded events a 0.1% subset is eight dots, and eight dots have a relative standard error
near 35% before any biology is considered — so a two-fold difference between conditions
is not measurable, whatever the gate says. Those are facts, and they are handed to the run as
facts it must reconcile one by one, then checked back against its answer afterwards.
What it does not do: it never reads your event data, so it cannot see a clog, a gate, a
cluster or a real MFI. It cannot tell you whether your antibody titre was right or whether
your cells were alive. And it does not run software — there are no commands anywhere in
this app's output, by design.