The LabKey Flow module automates high-volume flow cytometry analysis. It is designed to manage large data sets from standardized assays spanning many instrument runs that share a common gating strategy.

To begin using LabKey Flow, an investigator first defines a gate template for an entire study using FlowJo, and uploads the FlowJo workspace to the LabKey Server. He or she then points LabKey Flow to a repository of FCS files on a network file server, and starts an analysis.

LabKey Flow computes the compensation matrix, applies gates, calculates statistics, and generates graphs. Results are stored in a relational database and displayed using secure, interactive web pages.

Researchers can then define custom queries and views to analyze large result sets. Gate templates can be modified, and new analyses can be run and compared. Results can be printed, emailed, or exported to tools such as Excel or R for further analysis. LabKey Flow enables quality control and statistical positivity analysis over data sets that are too large to manage effectively using PC-based solutions.

LabKey Flow is not well-suited for highly interactive, exploratory investigations with relatively small sample sizes. We recommend FlowJo for that type of analysis. LabKey Flow is in production use at the McElrath Lab at FHCRC and the Wilson Lab at the University of Washington.

Documentation Topics

• Flow Cytometry Overview
• Includes:
• Advantages of using LabKey Flow
• How LabKey Flow works with FlowJo
• Two basic pathways for leveraging LabKey Flow for flow analyses.
• Flow Team Members
• Tutorial: Import a Flow Workspace
• Set up a Server and the Flow Demo Project
• Step 1: Set Up a Flow Folder
• Step 2: Upload Files to Server
• Step 3: Import a Flow Workspace and Analysis
• Step 4: Customize Your Grid View
• Step 5: Examine Graphs
• Step 6: Examine Well Details
• Step 7: Export Flow Data
• Tutorial: Perform a LabKey Flow Analysis
• Step 1: Define a Compensation Calculation
• Step 2: Define an Analysis
• Step 3: Apply a Script
• Step 4: View Results
• Custom Flow Queries
• Create Custom SQL Queries
• Add Statistics to FCS Queries
• Calculate Suites of Statistics for Every Well
• Flow Module Schema

Academic papers

• Development of an automated analysis system for data from flow cytometric intracellular cytokine staining assays from clinical vaccine trials