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SPADE / Spanning tree Progression of Density normalized Events

Facilitates the analysis of cellular heterogeneity, the identification of cell types, and comparison of functional markers in response to perturbations, based on a versatile method. SPADE helps to organize high-dimensional cytometry data in an unsupervised manner, and to investigate natural and pathogenic cellular heterogeneity for biological insight. The SPADE algorithm consists of four components: (i) density-dependent downsampling, (ii) clustering, (iii) linking clusters with a minimum spanning tree, and (iv) upsampling to restore all cells in the final result. This modularized process allows more efficient sub-algorithms to replace the current components. In this sense, SPADE can be viewed as a framework for cytometric data analysis and visualization that has the capacity to be evolved and adapted.


Synthesizes low-dimensional visualizations of flow cytometry data. SANJAY is an algorithmic approach for automatically synthesizing 2D and 3D visualizations of high-dimensional flow cytometry data. It employs automated algorithmic synthesis techniques and symbolic decision procedures to create low-dimensional projections of high-dimensional data that can be easily visualized. Results synthesized by SANJAY were better than those produced by the multi-dimensional scaling and random projections approaches in terms of the maximum distortion in the pairwise distances.


Analyzes flow or mass cytometry data using a self-organizing map. Using a two-level clustering and star charts, FlowSOM helps to obtain a clear overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise. The algorithm consists of four steps: reading the data, building a self-organizing map, building a minimal spanning tree and computing a meta-clustering. We proposed several visualization options: star charts to inspect several markers, pie charts to compare with manual gating results, variable node sizes dependent on the amount of cells assigned to the node and a grid or a tree structure which both give topological information.