Flow Visualization and Compensation

Plot types, the hierarchy tree view, axis scaling, overlays, and fluorescence compensation.

Plot Types

• Scatter (dot plot) shows each event as a point
• Density is color-coded by event density and reads better on large datasets
• Contour draws iso-density lines for a topographic view that highlights cluster boundaries
• Histogram shows a single-parameter distribution curve

Add a plot to the workspace with Add Plot in the toolbar.

Hierarchy Tree View

Plots are arranged in a tree that mirrors your gating strategy. The root plot sits at the top, and child plots branch downward with connecting arrows labeled with the gate names and population percentages.

• Zoom and pan by scrolling and dragging, like a map
• Minimap appears in the corner on large trees; click anywhere on it to jump
• Focus mode zooms in on a single plot and dims the rest. Arrow keys move you between plots in the hierarchy while focused.
• Overview fits the entire tree back into view
• Gating path above the plots shows the chain from "All Events" down to the current selection (e.g., All Events → Lymphocytes → CD3+ → CD4+); click any step to jump

Number keys 1–9 switch between plots quickly.

Drill Down

Double-click a gate on any plot to create a child plot beneath it. Conspecta automatically picks the next set of parameters (preferring fluorescence channels you haven't used yet) and applies a sensible axis scale. This is the fastest way to build a multi-level gating strategy.

Axis Scales

Each axis can use one of four scales:

• Linear for scatter and other linear-range parameters
• Logarithmic for traditional log-scale fluorescence
• Biexponential for compensated data that includes negative values
• Arcsinh for hyperbolic-arcsine scaling, often preferred for mass cytometry and spectral flow

Switch the scale per axis from the plot toolbar; the change applies to all child plots that inherit from this one.

Population Overlays

Overlay any gated population onto a plot to compare it visually. Click Overlays in the plot toolbar and check the populations to show. Each overlay draws in its gate color so they're easy to distinguish.

• On histograms, overlays appear as separate distribution curves
• On scatter, density, and contour plots, overlays highlight the population's events
• Clear all removes every overlay at once

Density Color Schemes

Density and contour plots offer multiple color schemes: Jet, Viridis, Plasma, Inferno, Magma, and Grayscale. Pick whichever reads best for your figure or audience.

File Overlays on Histograms

When you have more than one file loaded, overlay the same parameter from other files on a histogram to compare distributions across samples. Click Files in the plot toolbar and pick the files to overlay. Each file gets its own color, and curves are normalized to percent-of-max so distributions with different event counts stay comparable.

Selections are per-plot, so different histograms can compare different sample sets.

Compensation

Spillover between fluorescence channels is the central challenge of multi-color flow. Conspecta gives you two compensation paths.

Compensation Wizard

If your FCS file contains an embedded spillover matrix (the $SPILLOVER or SPILL keyword), the Compensation section in the sidebar shows an Apply Compensation button. Click it to open the wizard:

• View the spillover matrix as a heatmap
• Edit values directly if you need to tweak
• Apply or remove compensation in one click and watch the plots redraw
• Import a CSV matrix from another tool
• Export the matrix to CSV

A green indicator appears in the sidebar when compensation is active.

Auto-Compute

For cases where the embedded matrix isn't optimal, or when there isn't one at all, the wizard can auto-compute a compensation matrix directly from your data. Pick the fluorescence parameters to include, run the computation, and review the matrix before applying.

Zoom Controls

Every plot has a small toolbar in the top-right with Zoom In, Zoom Out, and Reset. Use the mouse wheel to zoom and drag to pan. When a plot is focused:

• + or = zooms in
• - zooms out
• 0 resets to default

Next Steps

• Analyze flow cytometry for FCS upload, gating, and parameters
• Flow advanced analysis for dimensionality reduction, clustering, and derived parameters
• Flow reporting for statistics, exports, and reports