Introduction to FlowSOM in Cytobank

FlowSOM is an algorithm that speeds time to analysis and quality of clustering with Self-Organizing Maps (SOMs) that can reveal how all markers are behaving on all cells, and can detect subsets that might otherwise be missed. It clusters cells (or other observations) based on chosen clustering channels (or markers/features), generates a SOM of clusters, produces a Minimum Spanning Tree (MST) of the clusters, and assigns each cluster to a metacluster, effectively grouping them into a population. The FlowSOM algorithm outputs SOMs and MSTs showing population abundances and marker expression in various formats including pie charts, star plots, and channel-colored plots. Cytobank has extended the functionality to automatically create a new experiment using files written out of FlowSOM that include the original channels plus the addition of cluster and metacluster ID channels, to allow interaction with the cluster and metacluster output. Read the original FlowSOM publication by Van Gassen et al, Cytometry A (2015).


Here are some resources to learn more about FlowSOM:

How to Configure and Run a FlowSOM Analysis

Analysis and Interpretation of FlowSOM Results

How to Automatically Gate Cluster Channels

Display of FlowSOM Clusters on viSNE maps

The Effect of FlowSOM Settings on Run Time


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