We develop and apply new imaging tools (including spatial transcriptomics and genomics) to understand how gene regulation information propagates across scales from the molecular events within the nucleus to the organization of cells into tissues and organs, up to the scale of animal behavior. We aim to push the MERFISH technology to image a the level whole organ image as well as integrate the technology with other cutting edge neuroscience tools (retroviral tracing, calcium imaging, etc.).
Current projects in the lab include identification of the molecular basis of Neuroregeneration, determining the transcriptomics/connectivity role of the Thalamus within the Opioid addiction/withdrawal circuitry, developing a quantitative spatial readout for Huntingtons CAG expansions. On our technological development front, we are working on expanding our imaging area by an order of magnitude (MERFISH+), MERFISH imaging of thick tissue (200um+) with epifluorescence microscopes, MERFISH-based CRISPR pooled screening, and generating a retroviral tools for enabling MERFISH compatible single cell spatial connectomics.
We also am working on a web browser based MERFISH visualizer that runs locally and provides the with quantifications on their data (courtesy of Kresna Jenie) which can be found at https://www.merfisheyes.com/
UPDATES
May 12. 2026
MERFISH+ Microscope Building Series Video Released
April 28, 2026
“Spatial organization and detection of social orders in mouse primary olfactory system. ” Cell
https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
“A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain.” Cell
https://www.cell.com/action/showPdf?pii=S0092-8674%2826%2900387-9
March 12, 2026
“Whole-embryo spatial Transcriptomics at subcellular resolution from gastrulation to organogenesis.” Science (https://doi.org/10.1126/science.adt3439)
December 5, 2025 – Human Basal Ganglia Atlas using MEFISH+ vs Stereo-seq Preprint on bioRxiv – (https://www.biorxiv.org/content/10.64898/2025.12.02.691876v1)
November 4, 2025 – MERFISH+ Preprint on bioRxiv – (https://www.biorxiv.org/content/10.1101/2025.11.02.686137v1)
August 30, 2025 – A tiny new collaborator has joined our extended lab family! Welcome to the world, little Lux Nafisi!
September 26, 2025 – Jenny Dong passes her Candidacy Exam!
July 31, 2025 – Jie (Jess) Cui passes her Qualifying Exam!
May 23, 2025 – Samuel S. Park passes his Candidacy Exam!
January 8, 2025 – Yuanyi Dai, PhD. joins the Lab!
Recent presentation: