MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart Article Swipe
Colin Kern
,
Qingquan Zhang
,
Yifan Lu
,
Jacqueline Eschbach
,
Zehua Zeng
,
Elie N. Farah
,
Chu‐Yi Tai
,
Kai-Fu Yang
,
Ignatius Jenie
,
Fenyong Yao
,
Zoey Zhao
,
Qixuan Ma
,
Christopher M. Padilla
,
Alexander Monell
,
Siavash Moghadami
,
Fugui Zhu
,
Bin Li
,
Albert Yick Hou Lim
,
Grant Tucker
,
David Ellison
,
C. Neil
,
Xiaojie Qiu
,
Quan Zhu
,
Bogdan Bintu
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.11.02.686137
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.11.02.686137
Summary 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 Summary MERFISH+ 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. Highlights MERFISH+ expands MERFISH capabilities to measure >1,800 genes and at whole-organ 3D imaging scale Combines chemical probe anchoring with high-throughput volumetric microscopy and microfluidics Generates a 3D molecular atlas of a developing human heart with > 3.1 million cells at subcellular resolution Introduces Spateo-VI, a novel generative framework integrating 3D multimodal datasets
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- article
- Landing Page
- https://doi.org/10.1101/2025.11.02.686137
- https://www.biorxiv.org/content/biorxiv/early/2025/11/04/2025.11.02.686137.full.pdf
- OA Status
- green
- References
- 97
- OpenAlex ID
- https://openalex.org/W4415877408
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4415877408Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2025.11.02.686137Digital Object Identifier
- Title
-
MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heartWork title
- Type
-
articleOpenAlex work type
- Publication year
-
2025Year of publication
- Publication date
-
2025-11-04Full publication date if available
- Authors
-
Colin Kern, Qingquan Zhang, Yifan Lu, Jacqueline Eschbach, Zehua Zeng, Elie N. Farah, Chu‐Yi Tai, Kai-Fu Yang, Ignatius Jenie, Fenyong Yao, Zoey Zhao, Qixuan Ma, Christopher M. Padilla, Alexander Monell, Siavash Moghadami, Fugui Zhu, Bin Li, Albert Yick Hou Lim, Grant Tucker, David Ellison, C. Neil, Xiaojie Qiu, Quan Zhu, Bogdan BintuList of authors in order
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https://doi.org/10.1101/2025.11.02.686137Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2025/11/04/2025.11.02.686137.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2025/11/04/2025.11.02.686137.full.pdfDirect OA link when available
- Cited by
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0Total citation count in OpenAlex
- References (count)
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97Number of works referenced by this work
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