Example Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) data from the mouse colon

Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) is a massively multiplexed single-RNA-molecule imaging technique capable of spatially resolved single-cell transcriptomic profiling of thousands of genes in millions of cells within intact tissue slices. Initially introduced for brain tissues, MERFISH has since been extended to other tissues, where rapid RNA degradation during the preparation process can pose challenges. The companion paper to these example data outlines the application of MERFISH in one such challenging tissue, the mammalian gastrointestinal tract. The example data contained here represent raw MERFISH images and associated metadata necessary to illustrate the analysis pipeline that identifies RNAs from such data. , , , # Imaging the intestinal transcriptome with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH)

Paolo Cadinu
Jeffrey R. Moffitt
Boston Children's Hospital, 2025

## Description

This repository contains a subset of a raw MERFISH measurement of the mouse gastrointestinal tract. The images, metadata, and example scripts are designed to illustrate the use of an existing analysis pipeline for MERFISH raw data decoding. These data are provided as a companion dataset to the detailed instructions and protocols provided in Cadinu, Yang, Xu, et al., Current Protocols 2025.

## Main folder

This folder contains a set of raw image and metadata files derived from a MERFISH measurement.
\-- .tif files represent image stacks taken from individual fields of view at different hybridization rounds and saved on one of two different cameras
\-- .xml files contain metadata associated with the hardware settings used to collect the image stack

### Settings folder

This folder contains fil...