Project Overview
A spatial transcriptomics pipeline for analyzing MERFISH imaging outputs, including clustering, spatial niche identification, transcript mapping, differential expression analysis, and automated visualization tools.
In Fall 2024, the Bonsai biology team developed a comprehensive spatial transcriptomics pipeline to analyze data generated using MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization) technology. MERFISH is a state-of-the-art method that identifies and quantifies thousands of RNA molecules within tissue samples at single-cell resolution. The pipeline was meticulously crafted to process MERFISH outputs by performing tasks such as mapping cells back to a reference atlas for identification through Leiden clustering, identifying cellular neighborhoods using spatial data, precisely linking RNA transcripts to their cellular origins, and conducting differential expression analysis to uncover genes that are highly over-expressed or under-expressed within specific cell types.
To enhance usability, the team created an automated visualization suite that explores data in Euclidean, UMAP, and PCA spaces, along with generating gene expression charts. These tools are being actively used at the Miami Project to Cure Paralysis to study models of Experimental Autoimmune Encephalomyelitis (EAE) and Traumatic Brain Injury (TBI), driving meaningful insights in neurological research Biology.
