FCS Express can perform the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm.  The transformation allows for direct analysis and visualization for highly multiparametric single-cell flow, image, and mass cytometry data.


The final result of the algorithm in FCS Express is a heat map in which the positions of cells in related nodes are positioned within a hierarchical minimum spanning tree. Heat maps can be modified easily for improved visualization of populations while Gates may be created to identify node(s) of interest.


SPADE was developed at Stanford University by members of the Plevritis and Nolan laboratories.


More details on SPADE can be found in the following publications:

Qiu, P., et al. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat. Biotech. 29, 886-891 (2011).

Qiu, P. Inferring phenotypic properties from single-cell characteristics. PLoS One. 5, Web (2012).


To begin working with SPADE in FCS Express, please see the topics on:

Defining SPADE

Working with SPADE