Whole-mouse clearing and imaging at the cellular level with vDISCO
Open accessAbstract
Homeostatic and pathological phenomena often affect multiple organs across the whole organism. Tissue clearing methods, together with recent advances in microscopy, have made holistic examinations of biological samples feasible. Here, we report the detailed protocol for nanobody(V H H)-boosted 3D imaging of solvent-cleared organs (vDISCO), a pressure-driven, nanobody-based whole-body immunolabeling and clearing method that renders whole mice transparent in 3 weeks, consistently enhancing the signal of fluorescent proteins, stabilizing them for years. This allows the reliable detection and quantification of fluorescent signal in intact rodents enabling the analysis of an entire body at cellular resolution. Here, we show the high versatility of vDISCO applied to boost the fluorescence signal of genetically expressed reporters and clear multiple dissected organs and tissues, as well as how to image processed samples using multiple fluorescence microscopy systems. The entire protocol is accessible to laboratories with limited expertise in tissue clearing. In addition to its applications in obtaining a whole-mouse neuronal projection map, detecting single-cell metastases in whole mice and identifying previously undescribed anatomical structures, we further show the visualization of the entire mouse lymphatic system, the application for virus tracing and the visualization of all pericytes in the brain. Taken together, our vDISCO pipeline allows systematic and comprehensive studies of cellular phenomena and connectivity in whole bodies.
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Many diseases, including obesity, have systemic effects that perturb multiple organ systems throughout the body.
“Many diseases, including obesity, have systemic effects that perturb multiple organ systems throughout the body1,2.”
From A deep-learning framework reveals whole-body perturbations at cell level (2026) · cites this paper as [2]
Advanced tissue-clearing methods combined with fluorescence microscopy have enabled the visualization of large samples, including entire mouse bodies and big human tissue specimens at the single-cell resolution.
“Advanced tissue-clearing methods combined with fluorescence microscopy have enabled the visualization of large samples, including entire mouse bodies and big human tissue specimens at the single-cell resolution1–5.”
From A deep-learning framework reveals whole-body perturbations at cell level (2026) · cites this paper as [2]
vDISCO with GFP-Nanobooster labelling amplifies the endogenous eGFP signal and shifts it into the far-red spectrum, substantially improving signal-to-noise ratios throughout the tissue.
“This approach amplifies the endogenous eGFP signal in reporter mice and shifts it into the far-red spectrum, substantially improving signal-to-noise ratios throughout the tissue.”
From A deep-learning framework reveals whole-body perturbations at cell level (2026) · cites this paper as [2]
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A deep-learning framework reveals whole-body perturbations at cell level
Kaltenecker, D., Horvath, I., Al-Maskari, R., Chen, Y., Kolabas, Z. I., Hoeher, L., Todorov, M., Minde, D.-P., Kapoor, S., Turhan, S. G., et al. (2026) · Nature · doi:10.1038/s41586-026-10535-2 · Cited by 5 · see citing works
Self-citation
- Authors
- Cai, R., Kolabas, Z. I., Pan, C., Mai, H., Zhao, S., Kaltenecker, D., Voigt, F. F., Molbay, M., Ohn, T.-L., Vincke, C., Todorov, M. I., Helmchen, F., Van Ginderachter, J. A., & Ertürk, A.
- Affiliations
- Helmholtz Munich (DE)
- University of Zurich (CH)
- Vrije Universiteit Brussel (BE)
- Corresponding author
- Ertürk, Ali
- ORCID
- Venue
- Nature Protocols
- Published
- 2023-01-25
- Volume
- 18
- Issue
- 4
- Pages
- 1197-1242
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W4317952698
- Cited by
- 83
- References
- 74
- Citations by year
- 2026: 20 · 2025: 26 · 2024: 30 · 2023: 7
- FWCI
- 2.71
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Protocols (publishedVersion)
- PubMed (publishedVersion)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion)
- Open access LMU (Ludwid Maxmilian's Universitat Munchen) (submittedVersion)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion)
- VUBIR (Vrije Universiteit Brussel) (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- Deutsche Forschungsgemeinschaft (EXC 2145)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Zebrafish Biomedical Research Applications
- Keywords
- tissue clearing, cellular resolution imaging
- MeSH terms
- Animals, Brain, Coloring Agents, Microscopy, Fluorescence, Solvents, Neurites, Imaging, Three-Dimensional, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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