Flow Reporting and Export

Statistics, exports, metadata, annotations, and data-quality warnings.

Statistics Panel

Select any gate to see its statistics in the panel beneath the plot area. The panel auto-expands when you select a new gate and collapses when you don't need it.

Use the Columns button to pick what appears in the table:

Population-level

• Event count, % of parent, % of total

Per parameter

• Mean, median, geometric mean
• Standard deviation, coefficient of variation (%CV), robust CV (rCV) using median absolute deviation
• Min, max, Q1, Q3, interquartile range (IQR)
• Percentiles P5, P10, P90, P95
• Skewness and kurtosis
• Distribution histogram column for inline shape inspection

Clipboard Copy

Copy statistics to your clipboard for pasting into Excel, Prism, or anywhere else:

• Copy Table copies the entire statistics table in CSV format
• Copy Selected copies just the rows you've highlighted (tab-separated for clean Excel paste)

Click a row to select it. Cmd/Ctrl+click adds rows; Shift+click selects a range.

Spreadsheet Export

Export the full statistics table as Excel (.xlsx) for downstream analysis in R, Python, GraphPad Prism, FlowJo, or anywhere else. Click Export in the statistics panel.

The exported file includes:

• Every gate population with event counts, percentages, and every enabled statistic
• Red-highlighted cells for data-quality issues (parameter saturation, %CV above 50%)
• Amber-highlighted cells for gates with very few events
• Gate justification notes in a dedicated column, so the rationale travels with the data
• A color legend at the bottom of the sheet

FCS Population Export

Export gated populations back out as FCS files for sorting validation or downstream analysis in other software.

• Single gate exports one population at a time from the bottom statistics panel
• Multi-gate export opens a dialog box listing every gate with checkboxes, event counts, and filename previews. Select the gates you want and click Export Selected to download one FCS file per gate. Select All exports every population at once.

Exported files are named {original}__{gate_name}.fcs so they trace back to the source. The exported FCS file also gets a GATE_NAME keyword so downstream tools can find which population it came from.

Plot Export

Export individual plots, or every plot in the workspace, as publication-ready images.

1. Click the export button on any plot's toolbar
2. Choose PNG (raster) or SVG (vector, editable in Illustrator or Inkscape)
3. Customize the title, axis labels, font (Arial, Times New Roman, Helvetica, Courier), background color, and scale factor
4. Toggle Include Gates to decide whether gate overlays appear
5. Pick All Plots to export everything at once

Tree Export

Export the full hierarchy tree as a single artifact for presentations and manuscripts. Click Export in the tree toolbar and pick:

• PNG for a high-resolution raster
• PDF for a vector document
• Word (DOCX) for embedding directly into a manuscript

Set a title, decide whether to include a statistics table beneath the tree, and choose a scale factor.

Statistics Charts

Open Statistics Charts from the sidebar to visualize gate statistics as bars, comparisons, or correlation plots. Each chart can be:

• A bar chart, grouped bar, scatter, heatmap, paired, or dot strip
• Annotated with statistical tests (t-test, Mann–Whitney, ANOVA, Kruskal–Wallis, and others) with p-value brackets drawn between groups
• Decorated with regression lines and correlation coefficients (for scatter)

Add multiple charts, reorder them, and give each one a custom title. Statistics charts feed directly into Figures when you want a final layout.

Data-Quality Warnings

Conspecta auto-checks each analysis for common issues and shows warnings at the top of the workspace:

• Compensation matrix present but not applied
• Unusual parameter ranges or signal saturation
• Low event counts in critical populations

Warnings are informational. They highlight risks but don't block your work.

Experiment Metadata

Open the Metadata panel in the sidebar to record context for the analysis. Conspecta provides seven standard fields out of the box:

• Experiment date
• Instrument
• Operator
• Condition
• Timepoint
• Patient ID
• Panel (the staining panel)

You can add unlimited custom key/value fields beyond those. FCS file keywords from the source files are available as a separate read-only view.

Annotations

Gate Notes

Add a note to any gate to document your gating rationale. In the Populations panel, hover a gate row to find the note icon, click it, and type something like "set at FMO + 2 SD" or "based on isotype control". Gate notes appear in the statistics panel, in spreadsheet exports, and in the PDF tree export.

Tree Annotations

Draw directly on the hierarchy tree to highlight regions, add arrows, or write freehand notes. The annotation tools live in the sidebar (text, arrow, freehand, shapes). Annotations save with the analysis and appear in tree exports. Undo and redo cover both gate edits and annotations.

Keyboard Shortcuts

Next Steps

• Analyze flow cytometry for FCS upload, gating, and parameters
• Flow visualization for plot types and compensation
• Flow files and templates for multi-file workflows and QC
• Build figures to compose statistics charts and tree exports into a final figure