Boosting multiplexing capabilities for error-robust spatial transcriptomic methods using a set exchange approach

In the last decades, image-based transcriptomic and proteomic experiments have moved from single-target probes to multiplexed experiments, allowing researchers to study hundreds or even thousands of mRNA and protein targets simultaneously. This large increase in scope necessitates methods in either increased specificity or in error-correction, such as the Hamming Codes utilized in the imaging-based spatial transcriptomic method MERFISH. For some experimental conditions, Hamming Codes are efficient in encoding the highest possible number of genes for spatial analysis. However, for most experimental parameters, the optimal generation of error-robust codebooks is an unsolved mathematical problem. Here we present a method to generate highly optimized Extended Hamming Codebooks compatible with established error-correctable methodologies such as MERFISH. Our method uses an iterative set-exchange approach and generally reaches over 90% of the theoretical maximum limit of gene set complexity. W..., , , # Boosting multiplexing capabilities for error-robust spatial transcriptomic methods using a set exchange approach

[https://doi.org/10.5061/dryad.zkh1893m5](https://doi.org/10.5061/dryad.zkh1893m5)

We deposit a host of error-robust constant weight binary codebooks for Hamming Weights (HW) 4, 5, and 6, that are ready-to-use with current MERFISH (Multiplexed-Error-Robust-Fluorescence-In-Situ-Hybridization) methodologies. Each codebook is supplied both as a binary version and as a set-based version, and is accompanied by a file with metadata and a reordered version that maximizes the Hamming Distance of the earliest appearing rows. See below for full details of file organization.

## Description of the data and file structure

The data is associated with a manuscript in Science Advances, intending to create optimized error-robust constant-weight binary codebooks for given parameter combinations. 

The manuscript is titled: Boosting Multiplexing Capabilities for Error-Robust Spatial Trans...,