Workshop Description (Advanced Course)

MERFISH and seqFISH are new techniques for measuring 100s to 1000s of gene expression levels in-situ with high sensitivity and specificity. This workshop covers a detailed introduction to the methodology, and what goes into experimental design/execution.


Workshop Materials

Overview of the methods and examples of their usage. Introduction to oligo design of probes using in smFISH. Hands on example design workflow in MATLAB.

Continued oligo design and lecture on sample preparation.

Data analysis workflow for MERFISH.

Technical Requirements

The workshop does not require any prior knowledge, but basic MATLAB and extensive Python are used and application of MERFISH requires knowledge of these.


Dr. Rob Foreman is a postdoctoral scholar in the lab of Dr. Roy Wollman, Department of Chemistry and Biochemistry. Rob is developing a multiplexed smFISH measurement technique. He wants to use this technique to observe how cells are distributed in a joint gene expression state-space in order to pose questions about these distributions. Email:



Workshop Details

Prerequisites: None
Length: 3 days, 3 hrs per day
Level: Advanced
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 15

Spring 2020 Dates

May 19, 20, and 21
9:00 AM to 12:00 PM