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.

Gradinaru lab publications in PubMed and bioRxiv.


CRISPR-clear imaging of melanin-rich B16-derived solid tumors

April 4 2023, Communications Biology

Schubert R, Bae T, Simic B, Smith SN, Park S-H, Nagy-Davidescu G, Gradinaru V, Plückthun A, Hur JK


Light-guided sectioning for precise in situ localization and tissue interface analysis for brain-implanted optical fibers and GRIN lenses

Sep 28, 2021, Cell Rep

Kahan A, Greenbaum A, Jang MJ, Robinson JE, Cho JR, Chen X, Kassraian P, Wagenaar DA, Gradinaru V.

The SHREAD gene therapy platform for paracrine delivery improves tumor localization and intratumoral effects of a clinical antibody

May 25, 2021, PNAS 

Sheena N. Smith, Rajib Schubert, Branko Simic, Dominik Brücher, Markus Schmid, Niels Kirk, Patrick C. Freitag, Viviana Gradinaru, and Andreas Plückthun


Tissue clearing and its applications in neuroscience

January 2, 2020, Nature Reviews Neuroscience

Hiroki R. Ueda, Ali Ertürk, Kwanghun Chung, Viviana Gradinaru, Alain Chédotal, Pavel Tomancak, Philipp J. Keller


Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies

April 26, 2019, Nature Communications

Pradeep S. Rajendran, Rosemary C. Challis, Charless C. Fowlkes, Peter Hanna, John D. Tompkins, Maria C. Jordan, Sarah Hiyari, Beth A. Gabris-Weber, Alon Greenbaum, Ken Y. Chan, Benjamin E. Deverman, Heike Münzberg, Jeffrey L. Ardell, Guy Salama, Viviana Gradinaru, Kalyanam Shivkumar


Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy

October 31, 2018, The Journal of Neuroscience

Tomoyuki Mano, Alexandre Albanese, Hans-Ulrich Dodt, Ali Erturk, Viviana Gradinaru, Jennifer B. Treweek, Atsushi Miyawaki, Kwanghun Chung, Hiroki R. Ueda

Hydrogel-Tissue Chemistry: Principles and Applications

May 24, 2018, Annual Review of Biophysics

Viviana Gradinaru, Jennifer Treweek, Kristin Overton, Karl Deisseroth


Q&A: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology?

September 25, 2017, BMC Biology

Alon Greenbaum, Min J. Jang, Collin Challis, Viviana Gradinaru

Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow

April 26, 2017, Science Translational Medicine

Alon Greenbaum, Ken Y. Chan, Tatyana Dobreva, David Brown, Deepak H. Balani, Rogely Boyce, Henry M. Kronenberg, Helen J. McBride, Viviana Gradinaru


Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling

September 27, 2016, mBio

William H. DePas, Ruth Starwalt-Lee, Lindsey Van Sambeek, Sripriya Ravindra Kumar, Viviana Gradinaru, Dianne K. Newman

Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors

July 6, 2016, Current Opinion in Biotechnology

Jennifer Brooke Treweek, Viviana Gradinaru

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing

June 24, 2016, Development

Sheel Shah, Eric Lubeck, Maayan Schwarzkopf, Ting-Fang He, Alon Greenbaum, Chang Ho Sohn, Antti Lignell, Harry M. T. Choi, Viviana Gradinaru, Niles A. Pierce, Long CaiarticleTroubleshooting


Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

October 19, 2015, Nature Protocols

Jennifer B Treweek, Ken Y Chan, Nicholas C Flytzanis, Bin Yang, Benjamin E Deverman, Alon Greenbaum, Antti Lignell, Cheng Xiao, Long Cai, Mark S Ladinsky, Pamela J Bjorkman, Charless C Fowlkes, Viviana Gradinaru


Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

July 31, 2014, Cell

Bin Yang, Jennifer B. Treweek, Rajan P. Kulkarni, Benjamin E. Deverman, Chun-Kan Chen, Eric Lubeck, Sheel Shah, Long Cai, Viviana Gradinaru