Tools

NovoSpaRc (de novo spatial reconstruction)

Embedding single cells (or, their single-cell RNA sequencing expression profile representation) into their original spatial context, or tissue of origin, based on structural similarities between the cells in high dimensional gene expression space and the cellular locations in physical space (and, if available, an imaging reference atlas), based on generalized optimal transport.

The code is available on github.

Related publication:

 

Nitzan, M.*, Karaiskos, N.*, Friedman, N. and Rajewsky, N. 2019. Gene expression cartography.

Nature, 576(7785), pp.132-137.

Moriel, N.*, Senel, E.*, Friedman, N., Rajewsky, N., Karaiskos, N., and Nitzan, M. 2021. NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport. Nature Protocols, pp. 1-24.