FlowJo 10 visualization and analysis software is designed to advance research in flow cytometry by providing tools for analysis automation and a bridge to repository/cloud-based data. Group organization, templates and command line tools provide an automation solution that can address the analysis bottleneck in clinical trials and high-throughput cytometry by organizing samples and batch analysis, maintaining consistent analysis for repeated SOP, reducing downtime caused by time spent in manual analysis and report generation, and increasing lab capability for high-throughput and high-content assays. The software has the ability to generate workspace templates. When data is placed into a template, samples are organized into groups, analysis executed, reports generated, and an analysis workspaces created and saved for review. The package can provide integration from the current paradigm of local file storage to accessing cloud/LIMS-based flow data for analysis, saving workspaces and exporting reports to the cloud/LIMS.