Analyze Flow Cytometry Data

The Flow workspace (under the Flow tab in Analysis) is a full flow cytometry analysis environment in your browser. Upload FCS files, build gating hierarchies, run compensation, do dimensionality reduction and clustering, and export publication-ready statistics. No desktop software required.

Uploading FCS Files

Conspecta accepts Flow Cytometry Standard (.fcs) files. Open Analysis → Flow, then click Import FCS or drag your files into the workspace. Files are parsed automatically and uploaded to your project.

Analysis Landing Page

Every analysis appears as a card on the Flow landing page with its name, file count, and last-modified date.

• Grid view shows visual cards
• Table view is sortable spreadsheet rows
• Folders group analyses by experiment, date, or sample
• Star to pin in-progress analyses
• Bulk select to move, delete, or organize many at once
• Sort and filter by name, dates, event count
• Move across projects when work crosses studies; the FCS files and preview travel with the analysis (see Moving work between projects)

Creating an Analysis

Click Import FCS, pick a file, and Conspecta creates an analysis named after it. The workspace opens with your first FCS file ready to gate. From there:

1. Pick your starting parameters (commonly FSC-A vs SSC-A)
2. Draw your first gate
3. Load additional files into the same analysis from the Files panel in the sidebar

Analyses save automatically. Click the analysis name in the sidebar to rename it, add notes, or see contributors.

Interactive Gating

Draw gates directly on plots to define populations. Each gate type has a keyboard shortcut for quick switching.

Gate Types

• Rectangle (R) for simple boxes
• Polygon (P) for freeform shapes around irregular populations
• Ellipse (E) for tightly clustered populations
• Quadrant (Q) to split a plot into four (common for dual-marker staining)
• Range (G) for a slice on a single axis (useful on histograms)
• Boolean gates combining existing gates with AND / OR / NOT (e.g., "CD4+ AND NOT CD8+")
• Singlets as a one-click button that draws a singlet gate from the area-vs-height diagonal

Gating Hierarchy

Gates nest into a tree that mirrors your full strategy:

All Events
  └─ Singlets (FSC-A vs FSC-H)
       └─ Live Cells (viability dye)
            ├─ CD4+ T Cells
            │    └─ CD4+ CD25+ (Tregs)
            └─ CD8+ T Cells

Each gate shows its event count and percentage of the parent population. The Populations panel on the right of the workspace displays the full tree:

• Gate-type icons so you can see the shape at a glance
• Percentage bars behind the gate name, colored by gate color and sized by % parent
• Collapse/expand for nested branches
• Parameter labels showing which axes the gate was drawn on

Backgating

Toggle backgating on any gate to highlight its events on every other plot in the tree. Use it to confirm a downstream population (CD4+ T cells, for example) lands where it should on upstream plots (FSC/SSC scatter).

Parameter Selection

Pick what to display on each axis. Available choices are:

• Scatter parameters like FSC and SSC (forward and side scatter)
• Fluorescence channels for whatever your panel includes (FITC, PE, APC, and so on)
• Compensated values once compensation is applied
• Derived parameters that you've created from formulas
• Virtual parameters from dimensionality reduction (UMAP, t-SNE, PCA) once those have run

Switching parameters is instant; the plot redraws against the new axes.

Renaming Parameters

FCS files often use cryptic channel names (FL1-H rather than CD4-FITC). Open Rename Parameters in the sidebar to assign human-readable aliases that follow your data everywhere: axis labels, statistics tables, and exports.

Next Steps

• Flow visualization for plot types, the hierarchy tree, and compensation
• Flow advanced analysis for dimensionality reduction, clustering, and specialized analyses
• Flow files and templates for multi-file workflows and reusable templates
• Flow reporting for statistics, exports, and reports