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]

Segmentation problems

Molecules

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

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