Baysor: segmentation of spatial transcriptomics data

Viktor Petukhov

Khodosevich lab, BRIC

How to map expression to space?

Spatial gene expression patterns

pciSeq

MERFISH

1. X. Qian, K.D. Harris, T. Hauling, D. Nicoloutsopoulos, A.M. Manchado, N. Skene, J. Hjerling-Leffler, M. Nilsson, bioRxiv 2018, 431957276097

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

[1]

[2]

• 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

*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)

Baysor: segmentation of spatial transcriptomics data

Expected

cell size

Transcript data

DAPI

Poly-A

staining

Optional

Baysor: Dirichlet Mixture Models over Markov Random Fields

Random field via triangulation

Baysor: Alorithm demonstration

Segmentation results

Local gene composition

Cell type

Segmentation results

Number of segmented cells

%of assigned molecules

Come to the poster for more details!

https://github.com/hms-dbmi/Baysor

Acknowledgments

• Sten Linnarson lab
• Mats Nilsson lab
• Long Cai lab
• Jeffrey Moffitt lab
• SpaceTx consortium

Konstantin Khodosevich lab

Peter Kharchenko