MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart

Kern, C.; Zhang, Q.; Lu, Y.; Eschbach, J.; Zeng, Z.; Farah, E. N.; Tai, C.-Y.; Yang, K.; Jenie, I.; Yao, F.; Zhao, Z.; Ma, Q.; Padilla, C. G.; Monell, A.; Moghadami, S.; Zhu, F.; Li, B.; Hou, A.; Tucker, G.; Ellison, D.; Chi, N. C.; Qiu, X.; Zhu, Q.; Bintu, B.

doi:10.1101/2025.11.02.686137

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bioRxiv · 10.1101/2025.11.02.686137

MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart

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Abstract

Hybridization-based spatial transcriptomics technologies have advanced our ability to map cellular and subcellular organization in complex tissues. However, existing methods remain constrained in gene coverage, multimodal compatibility, and scalability. Here, we present MERFISH+, an enhanced version of Multiplexed Error-Robust Fluorescence in Situ Hybridization (MERFISH), which integrates chemical probe anchoring in protective hydrogels with high-throughput microfluidics and microscopy. This optimized design supports robust and repeated hybridization cycles across an entire centimeter-scale tissue sample. MERFISH+ allowed to simultaneously quantify over 1,800 genes and resolve the 3D organization of chromatin loci and their associated epigenomic marks in developing human hearts. Using a generative integration framework for spatial multimodal data (Spateo-VI), we harmonized these MERFISH+ transcriptomic and chromatin data to reconstruct a 3D spatially-resolved multi-omic atlas of the developing human heart at subcellular resolution capturing 3.1 million cells across 34 distinct populations. This 3D atlas provides a holistic view of an entire organ enabling the characterization of 3D cellular neighborhoods and transcriptional gradients of substructures such as the descending arteries. Thus, MERFISH+ offers a robust, large-format platform for spatial multi-omics that enables high resolution mapping of gene expression at subcellular resolution and the characterization of cellular organization within 3D organs. One Sentence SummaryMERFISH+ is an spatial multi-omics platform that integrates hydrogel-based probe anchoring, automated high-throughput microfluidics, and large-format multimodal data production to enable comprehensive, subcellular resolution mapping of gene expression and chromatin organization across millions of cells within complex developing human organs. HighlightsO_LIMERFISH+ expands MERFISH capabilities to measure >1,800 genes and at whole-organ 3D imaging scale C_LIO_LICombines chemical probe anchoring with high-throughput volumetric microscopy and microfluidics C_LIO_LIGenerates a 3D molecular atlas of a developing human heart with > 3.1 million cells at subcellular resolution C_LIO_LIIntroduces Spateo-VI, a novel generative framework integrating 3D multimodal datasets C_LI

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Kern, C., Zhang, Q., Lu, Y., Eschbach, J., Zeng, Z., Farah, E. N., Tai, C.-Y., Yang, K., Jenie, I., Yao, F., Zhao, Z., Ma, Q., Padilla, C. G., Monell, A., Moghadami, S., Zhu, F., Li, B., Hou, A., Tucker, G., Ellison, D., Chi, N. C., Qiu, X., Zhu, Q., Bintu, B.. 2025-11-04. MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart. https://doi.org/10.1101/2025.11.02.686137

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