Blog
Insights on flow cytometry analysis, AI-assisted gating, and reproducibility in research.
When to Use FMO Controls in Flow Cytometry (and When Isotype Controls Won't Do)
FMO controls vs isotype controls: when each one belongs in your gating workflow, what they actually measure, and when to skip both.
Over-Compensation and Under-Compensation in Flow Cytometry: How to Spot Them
Seven compensation mistakes that pass auto-calculation: smeared negatives, tandem dye drift, and how to spot them before publishing.
Doublet Discrimination in Flow Cytometry: FSC-A vs FSC-H and SSC-W Gates
How to draw the singlet gate using FSC-A vs FSC-H, where it sits in your gating hierarchy, and what to do when only SSC-W is available.
Daily Instrument QC for Flow Cytometry: When and How to Use Calibration Beads
CS&T, Rainbow, and EQC beads for daily flow cytometry calibration: which to use, specific thresholds, and the daily startup procedure.
How to Find the Right Antibody Concentration for Flow Cytometry: Titration Protocol
Antibody titration protocol for flow cytometry: calculate Stain Index, run a serial dilution series, and find the optimal concentration for your panel.
Flow Cytometry QC: Tracking Instrument Performance Across Runs
Track flow cytometry QC metrics across instrument runs using Levy-Jennings charts. Specific thresholds, Westgard rules, and PMT voltage trend tracking.
Live/Dead Discrimination in Flow Cytometry: DAPI, PI, Fixable Dyes Compared
Cell viability gating DAPI vs live-dead stain — PI, 7-AAD, DAPI, and fixable amine dyes compared on channel, fixation, brightness, and cost.
Sharing Flow Cytometry Analysis Across Labs: Workspace Files and Reproducibility Pitfalls
FlowJo workspace file collaboration across labs — 7 pitfalls that break gates in transit and the open-format fixes that survive the journey.
Exporting Flow Cytometry Statistics for Papers: MFI, Percent Positive, and Gate Labels
How to export flow cytometry statistics for publication — MFI definitions, gate labels, Prism, Gating-ML 2.0, and MIFlowCyt — without reviewer churn.
Spectral vs Conventional Flow Cytometry: When the Upgrade Is Worth It
Spectral vs conventional flow cytometry: panel size, autofluorescence, cost, and a per-reader-type verdict on when the upgrade is worth it.
Reducing Gating Variability Between Operators: Templates, FMOs, and Automated Approaches
Reducing gating reproducibility variance between operators: FMOs, locked templates, automated gating, and concordance audits with concrete numbers.
How to Identify Cell Populations by Scatter Plot: An FSC/SSC Reference
How to identify cell populations by scatter plot: FSC and SSC reference for PBMCs, whole blood, bone marrow, and the limits of scatter-only gating.
Batch Processing FCS Files: A Practical Workflow for Multi-Sample Analysis
Batch process FCS files across multiple samples without silent failures: parameter mapping, compensation drift, template traps, and validation checks.
t-SNE and UMAP for Flow Cytometry: Reading High-Dimensional Cell Populations Correctly
t-SNE and UMAP flow cytometry dimensionality reduction: prerequisites, parameter tuning, and the interpretation pitfalls practitioners miss.
How to Analyze Rare Cell Populations in Flow Cytometry: Event Count, Gates, and Statistical Confidence
How to analyze rare cell populations in flow cytometry: event count math, Poisson CV formulas, dump channel gating, worked HSC and CTC examples.
Multicolor Flow Cytometry Panel Design: Fluorochrome Selection, Controls, and Spillover Rules
How to design a multicolor flow cytometry panel: markers, lasers, strength-matching fluorochromes, SSM-aware refinement, and FMO vs isotype controls.
How to Analyze FCS Files Without FlowJo: Free Tools, Programmatic Options, and What You Give Up
Practical guide to analyzing FCS files without a FlowJo license. Covers the FCS file format structure, free tools (FCS Express, Floreada, FCSalyzer), programmatic options (R flowCore, Python FlowKit), and what you actually give up when switching from FlowJo.
Flow Cytometry Data Analysis Software Comparison: A Decision Framework for Research, Clinical, and GxP Labs
Practical flow cytometry data analysis software comparison for 2025. Decision tree for research, clinical, and GxP labs comparing FlowJo, FCS Express, Kaluza, OMIQ, and R/Bioconductor by regulatory compliance, workflow fit, and total cost of ownership.
How to Compensate for Spectral Overlap in Flow Cytometry: Controls, Matrix Math, and Validation
Step-by-step guide to compensating for spectral overlap in flow cytometry. Includes a worked spillover matrix example with real coefficients, single-color control setup, compensation validation checks, and troubleshooting common errors.
AI-Assisted Gating in Flow Cytometry: What Is Real and What Is Hype
When does AI-assisted gating actually help in flow cytometry? Decision framework for automated gating approaches, accuracy benchmarks from recent studies, and what you need in place before adopting ML-based gating.
How to Set Up a Gating Strategy in Flow Cytometry: Sequential Gates, Back-Gating, and Reproducibility
Step-by-step guide to building a reproducible flow cytometry gating strategy. Covers time gates, scatter gating, doublet discrimination, FMO controls, back-gating validation, and troubleshooting common gating errors.
FlowJo Alternatives: What Core Facilities Are Actually Switching To
Comparing free and paid FlowJo alternatives for flow cytometry analysis. Feature matrix, switching criteria, and what actually matters for core facilities evaluating new software.