Tissue Clearing

We are developing improved methods for imaging through thick intact tissue samples at high resolution by rendering them optically transparent and permeable to stains, antibodies and nucleic acid probes.

PARS/PACT - for imaging large tissue sections Treewek et al., Nature Protocols 2015 [ Protocols.io link ]

N.B., modifications required for certain tissues including bone and sputum. See relevant publications for details.

  • The CLOVER Center is equipped with wet labs for tissue processing, macromolecular staining, and imaging.

  • CLOVER offers researchers on-site use of tissue clearing facilities and technical support.

CLOVER offers:

  • One-on-one consultations and training for tissue clearing techniques to jump start research projects.

  • Focused workshops for researchers with various backgrounds and experience levels

  • A yearly 5-day course on systemic AAVs and CLARITY as part of the NeuroNex MINT Technology Hub

Tissue Clearing Publications

  • Spatial transcriptomics for profiling the tropism of viral vectors in tissues. Jang M.J., Coughlin G.M., Jackson C.R., Chen X., Chuapoco M.R., Vendemiatti J.L., Wang A.Z., Gradinaru V. Nature Biotechnology, 2023; 10.1038/s41587-022-01648-w. [ Article | Research Briefing ]

  • Light-guided sectioning for precise in situ localization and tissue interface analysis for brain-implanted optical fibers and GRIN lenses. Kahan A., Greenbaum A., Jang M.J., Robinson J.E., Cho J.R., Chen X., Kassraian P., Wagenaar D.A., Gradinaru V. Cell Reports, 2021; doi: 10.1016/j.celrep.2021.109744. [ Article ]

  • The SHREAD gene therapy platform for paracrine delivery improves tumor localization and intratumoral effects of a clinical antibody. Smith S.N., Schubert R., Simic B., Brucher D., Schmid M., Kirk N., Freitag P.C., Gradinaru V., Plückthun A. Proceedings of the National Academy of Sciences, USA, 2021; doi: 10.1073/pnas.2017925118. [ Article ]

  • Tissue Clearing and Its Applications in Neuroscience. Ueda, H. R., Ertürk, A., Chung, K., Gradinaru, V., Chédotal, A., Tomancak, P., Keller, P. J., Nature Reviews Neuroscience, 2020; doi: 10.1038/s41583-019-0250-1.  [ Article ]

  • Low- and high-thermogenic brown adipocyte subpopulations coexist in murine adipose tissue. Song, A., Dai, W., Jang, M.J., Medrano, L., Li, Z., Zhao, H., Shao, M., Tan, J., Li, A., Ning, T., Miller, M.M., Armstrong, B., Huss, J.M., Zhu, Y., Liu, Y., Gradinaru, V., Wu, X., Jiang, L., Scherer, P.E., Wang, Q.A., J Clinical Investigations, 2020; doi: 10.1172/JCI129167. [Article ]

  • Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy. Mano, T., Albanese, A., Dodt, H.-U., Erturk, A., Gradinaru, V., Treweek, J. B., Miyawaki, A., Chung, K., Ueda, H. R. The Journal of Neuroscience, 2018, 38(44), 9330–9337; doi: 10.1523/jneurosci.1677-18.2018.  [ Article ]

  • Hydrogel-Tissue Chemistry: Principles and Applications. Gradinaru V, Treweek J, Overton K, Deisseroth K. Annu Rev Biophys. 2018 May 20;47:355-376; doi: 10.1146/annurev-biophys-070317-032905.  [ Article | Open access link ]

  • Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow. Greenbaum, A.*, Chan, K.Y.*, Dobreva, T., Brown, D., Balani, D.H., Boyce, R., Kronenberg, H.M., McBride, H.J., Gradinaru, V. Sci Transl Med, 2017; 9, eaah6518.  [ Article | Caltech News Release | Nature Research Highlights | Popular Science ]

  • Exposing the three-dimensional biogeography and metabolic states of pathogens in cystic fibrosis sputum via hydrogel embedding, clearing, and rRNA labeling. DePas, W.H., Starwart-Lee, R., Van Sambeek, L., Kumar, S.R., Gradinaru, V.*, Newman, D.K.* mBio, 2016; doi:10.1128/mBio.00796-16. [ Article | Caltech News Release | MiPACT Video]

  • Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors. Treweek, J.B., Gradinaru, V.  Curr Opin Biotechnol, 2016; 40, 193-207.  [ Article ]

  • Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing. Shah, S.*, Lubeck, E.*, Schwarzkopf, M.*, He, T.*, Greenbaum, A.*, Sohn, C.H., Lignell, A., Choi, H.M.T., Gradinaru, V., Pierce, N.A., Cai, L. Development, 2016; 90.  [ Article ]

  • Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. Treweek, J.B.; Chan, K.Y.; Flytzanis, N.C.; Yang, B.; Deverman, B.E.; Greenbaum, A.; Lignell, A.; Xiao, C.; Cai, L.; Ladinsky, M.S.; Bjorkman, P.J.; Fowlkes, C.C.; Gradinaru, V. Nat Prot, 2015; doi:10.1038/nprot.2015.122.  [ Article | Troubleshooting ]

19 Publications by other groups using CLARITY in FY2022 – 3 highlighted below:

  • Dense functional and molecular readout of a circuit hub in sensory cortex. C. Condylis, A. Ghanbari, N. Manjrekar, K. Bistrong, S. Yao, T.N. Nguyen, H. Zeng, B. Tasic, J.L. Chen Science 2022; 10.1126/science.abl5981.

  • Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis. C.R.Armbruster, C.W. Marshall, A.I. Garber, J.A. Melvin, A.C. Zemke, J. Moore, P.F.Zamora, K. Li, I.L. Fritz, C.D. Manko, M.L. Weaver, J.R. Gaston, A. Morris, B.Methe, W.H. DePas, S.E. Lee, V.S. Cooper, J.M. Bromberger Cell Reports 2021; 10.1016/j.celrep.2021.109829.

  • Differential H4K16ac levels ensure a balance between quiescence and activation in hematopoietic stem cells. C.P. Rodrigues, A. Akhatar Science Advances 2021; 10.1126/sciadv.abi5987.

19 Publications by other groups using CLARITY in FY2021 – 3 highlighted below:

  • Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior. Y. Kolsch, J. Hahn, A. Sappington, M. Stemmer, A.M. Fernandes, T.O. Helmbrecht, S. Lele, S. Butrus, E. Laurell, I. Arnold-Ammer, K. Shekhar, J.R. Sanes, H. Baier Neuron 2021; 10.1016/j.neuron.2020.12.003.

  • A neuroskeletal atlas: spatial mapping and contextualization of axon subtypes innervating long bones of C3H and B6 mice. M.R. Lorenz, J.M. Brazill, A.T. Beeve, I. Shen, E.L. Scheller Journal of Bone & Mineral Research 2021; 10.1002/jbmr.4273.

  • Value-guided remapping of sensory cortex by lateral orbitofrontal cortex." A. Banerjee, G. Parente, J. Teutsch, C. Lewis, F.F. Voigt, F. Helmchen Nature 2020; 10.1038/s41586-020-2704-z.

8 Publications by other groups using CLARITY in FY2020 – 2 highlighted below:

  • Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy. C. Prahst, P. Ashrafzadeh, T. Mead, A. Figueiredo, K. Chang, D. Richardson, L.Venkaraman, M. Richards, A. Martins Russo, K. Harrington, M. Ouarne, A. Pena, D.F. Chen, L. Claesson-Welsh, K. Cho, C.A. Franco, K. Bentley eLife 2020; 10.7554/eLife.49779.

  • Fungal biofilm morphology impacts hypoxia fitness and disease progression. C.H. Kowalski, J.D. Kerkaert, K. Liu, M.C. Bond, R. Hartmann, C.D. Nadell, J.E. Stajich, R.A. Cramer Nature Microbiology 2019; 10.1038/s41564-019-0558-7.

11 Publications by other groups using CLARITY in FY2019 – 3 highlighted below:

  • The role of accessory cells in islet homeostasis. Tang, S. C., Jessup, C. F., Campbell-Thompson, M. Current Diabetes Reports, 2018; 18:117; 10.1007/s11892-018-1096-z

  • High resolution 3D imaging of the human pancreas neuro-insular network. Butterworth, E., Dickerson, W., Vijay, V., Weitzel, K., Cooper, J., Atkinson, E. W., Coleman, J. E., Otto, K. J., Campbell-Thompson, M. Journal of Visualized Experiments, 2018; 131; 10.3791/56859

  • Quantitative assessment of regional variation in tissue clearing efficiency using optical coherence tomography (OCT) and magnetic resonance imaging (MRI): a feasibility study. Baek, K., Jung, S., Lee, J., Min, E., Jung, W., Cho, H. Scientific Reports, 2019; 10.1038/s41598-019-39634-z