Multiplexed Error Robust Fluorescence in Situ Hybridization(MERFISH)

Work Group

Project Lead(s)

Project Status


Project Deliverables

R/Bioconductor package, Repository of applications & downstream analyses and Interactive gallery of publicly available MERFISH datasets


HMS Department


Project Description

CCB worked on making MERFISH datasets accessible to the wider R/Bioconductor community, and connecting MERFISH data with the R/Bioconductor ecosystem of analysis packages and fostered new developments. This effort included first implementing access to publicly available MERFISH datasets from within R/Bioconductor and connecting the data package to novel ways of analyzing spatial transcriptomic data. Afterwards, the CCB team worked on connecting the data package and analysis results with integrative visualization tools to enable interactive exploration of segmentation, expression, and cell metadata on images.

Objectives: (1) develop an R/Bioconductor data package that implements single command actualization of MERFISH landmark datasets, (2) develop an RStudioConnect interface that enables interactive exploration of the data, (3) demonstrate applicability of novel analytic methods such as spatial graph analysis and cell-cell interaction analysis on MERFISH data.


Contact Sunil Poudel with questions about this project.