PhaseFinder
Session Control

Local FCS storage

PhaseFinder keeps browser-private FCS copies for fast session reload. They are not uploaded. Reloading the logo retains catalogued copies; Reset releases this session's copies.

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    FCS Files

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    Companion channels the pipeline will use — pick the right one for each if auto-detection is off:

    Pre-modeling QC Filtering

    Structural QC: Default saturation ceilings

    Time QC method: Robust summary QC

    Identify Peaks

    Plot a channel and check a sample in the table to identify peaks.

    Model & Fit

    CLOCCS fits each strain's timepoints together. Map the metadata columns that hold each sample's timepoint and (optionally) strain — the same columns the metadata table already shows.

    Histogram of Events
    Bins: 256
    128 256 512 1024
    Table of Loaded FCS Samples
    Column Operations
    Table I/O
    Column Removal

    Select the column(s) you want to delete by clicking their headers in the table.

    Columns to remove:
    (None)

    Filename to Metadata Wizard

    Filename Split Steps
    Preview

    Calculate Statistics

    Statistics

    Reconnect Session Files

      Scanning for missing FCS files in selected folder:

      Set Axis Range Limits

      X-Axis
      Y-Axis

      Leave a field empty to use the current auto-scaled display value. Pan and zoom are always display-only.

      2. Time QC Method

      Time QC method
      Channels to evaluate
      Advanced settings

      These defaults are tuned for typical acquisitions — you do not need to change them. Adjust only if you know the reason to; each field lists what it does and its default. Use Reset defaults to return every value to the shipped setting.

      1. Structural QC Settings

      Structural QC always rejects non-finite or negative readings. For the DNA-content channels it also rejects any event at or above a saturation ceiling, normally read straight from the FCS file's own recorded detector range ($PnR) for that channel. If a channel was repurposed as the DNA-content proxy, that recorded range can be stale or simply wrong — low enough to reject an entire real population (e.g. G2/M) as if it had saturated the detector, even when the raw histogram shows a clean, unclipped peak.

      DNA saturation ceiling

      Download Plot or Report

      Analysis report
      Vector (scales to any size, editable)
      Rasterized

      Bin size changed

      Recalculating all values…

      3. Cell Gate: Forward scatter vs Side scatter

      Drag the teal ellipse or its center marker to move the cell gate; hold Shift or Ctrl while dragging to rotate it around its center. Change coverage to resize it. Edits update the histogram and any peaks or fits.

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      Diagnostics
      
            
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