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Mai, H.* ; Wang, Y.* ; Zhu, Y.* ; Zhao, Y.* ; Chen, Y. ; Höher, L. ; Al-Maskari, R. ; Luo, J.* ; Ertürk, A.

Whole-mouse immunolabeling at cellular resolution for comprehensive 3D atlases.

Nat. Protoc., DOI: 10.1038/s41596-026-01363-9 (2026)
DOI PMC
Open Access Green as soon as Postprint is submitted to ZB.
Mapping complex biological systems and tracking disease progression at high resolution across the entire mammalian body has remained technically challenging. Here, to address this, we present wildDISCO (immunolabeling of wild-type mice and DISCO clearing), a comprehensive protocol for whole-body immunolabeling, optical clearing and imaging of mice at cellular resolution using standard IgG antibodies. This protocol optimizes tissue permeabilization using cyclodextrin as a potent enhancer of cholesterol extraction and membrane permeabilization, enabling deep antibody penetration across all organs. We detail procedures for sample preparation, tissue decolorization and decalcification, whole-body immunostaining, clearing, and subsequent 3D imaging, virtual reality visualization and whole-mouse atlas construction. The method allows comprehensive mapping of neuronal, vascular, lymphatic and immune systems, as well as systemic studies in disease models, including cancer and microbiome–host interaction studies. We anticipate that wildDISCO will serve as a broadly applicable platform for generating whole-body cellular atlases, enabling systems-level investigations of health and disease. Only standard immunohistochemistry facilities are required, but successful implementation may require initial technical training, particularly for researchers with limited prior experience in tissue clearing or 3D imaging workflows. From start to finish, the procedure takes 4 weeks.
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Publication type Article: Journal article
Document type Review
ISSN (print) / ISBN 1754-2189
e-ISSN 1750-2799
Journal Nature Protocols
Publisher Nature Publishing Group
Reviewing status Peer reviewed
Institute(s) Institute for Intelligent Biotechnologies (IBIO)