Massachusetts Institute of Technology

The Broad Institute, Inc.

The Weizmann Institute of Science

Nationaluniversity of Ireland, Maynooth

Luca D'Alessio

Mehrtash Babadi

Yonina Eldar

Ken Duffy

Litian Liu

A way to design a codebook for estimating the type of a molecule at a particular location in a fluorescence microscopy image makes use of one or both of (1) knowledge of the non-uniform prior distribution of molecule types (i.e., some types are known a priori to occur more frequently than others) and/or knowledge of co-occurrence of molecule types at close locations (e.g., in a same cell); and (2) knowledge of a model of the (e.g., random) process that yields the intensities that are expected at a location when a molecule with a particular subset of markers (i.e., a molecule of a type that has been assigned a codeword that defines that subset) is present at that location. The codebook design may provide experimental efficiency by reducing the number of images that need to be acquired and/or improve classification or detection accuracy by making the codewords for different molecule types more distinctive.

Coding for multiplexed fluorescence microscopy

Growing community of inventors

Cambridge, MA, United States of America

Luca D'Alessio