What is T-SNE?


High-dimensional single-cell technologies, such as multicolor flow cytometry,  mass cytometry, and image cytometry, can measure dozens of parameters at the single-cell level. FCS Express integrates t-Distributed Stochastic Neighbor Embedding, otherwise known as t-SNE, which is a tool that allows you to map high-dimensional cytometry data onto a two dimension plot while conserving the original high-dimensional structure to help you visualize and analyze high-dimensional data.


Using t-SNE Transformations in FCS Express

The final result of the algorithm in FCS Express is a 2D plot in which the positions of cells reflect their proximity in their original high-dimensional space. Plots can further be colored with density or heat mapping of each parameter, allowing for easy visualization of populations.

Given that t-SNE is an highly demanding algorithm, the De Novo Software 's team made a great effort to improve its speed within FCS Express.

To give you an idea of how t-SNE is performing within FCS Express, we have run some speed tests to show how the two methods that are used to calculate t-SNE compare with each other in version 6.

Learn more about tSNE in FCS Express via a recorded webinar.

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