Petukhov V, Xu RJ, Soldatov RA, Cadinu P, Khodosevich K, Moffit JR, Kharchenko P

Problem

How to map expression to space?

• Up to 10  cells
• Up to 10  transcripts
• Up to 10000 genes

Spatial protocols based on RNA-FISH or in situ sequencint

• DARTFISH
• ex-FISH
• StarMAP
• seq-FISH
• FISSEQ

Protocols

Data

6

7

Segmentation problems

Molecules

*Moffitt, J. R. et al. Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region. Science 362 (2018)

Segmentation problems

MERFISH

[1]

osm-FISH

[2]

1. Moffitt, J. R. et al. Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region. Science 362 (2018)

2. Simone Codeluppi, Lars E. Borm, Amit Zeisel, Gioele La Manno, Josina A. van Lunteren, Camilla I. Svensson & Sten Linnarsson. Nature Methods 15, 932–935 (2018)

Old results

Neighborhood composition

Segmentation across protocols

Segmentation across protocols

Benchmarking

New results

More benchmarks: pciSeq

MERFISH gut data

3D segmentation

Other plots

Thank you!