Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain

Synfire Chains and Cortical Songs: Temporal Modules of Cortical Activity

Ikegaya, Y., Aaron, G., Cossart, R., Aronov, D., Lampl, I., Ferster, D., & Yuste, R. (2004) · Science · doi:10.1126/science.1093173 · Cited by 838

Structural and molecular interrogation of intact biological systems

Chung, K., Wallace, J., Kim, S.-Y., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., Mirzabekov, J. J., Zalocusky, K. A., Mattis, J., Denisin, A. K., et al. (2013) · Nature · doi:10.1038/nature12107 · Cited by 2,008

Going deeper than microscopy: the optical imaging frontier in biology

Ntziachristos, V. (2010) · Nature Methods · doi:10.1038/nmeth.1483 · Cited by 1,896

Identification and classification of hubs in brain networks

Sporns, O., Honey, C. J., & Kötter, R. (2007) · PLoS ONE · doi:10.1371/journal.pone.0001049 · Cited by 1,165

Clarifying Tissue Clearing

Richardson, D. S., & Lichtman, J. W. (2015) · Cell · doi:10.1016/j.cell.2015.06.067 · Cited by 1,095

Three-dimensional imaging of solvent-cleared organs using 3DISCO

Ertürk, A., Becker, K., Jährling, N., Mauch, C. P., Hojer, C. D., Egen, J. G., Hellal, F., Bradke, F., Sheng, M., & Dodt, H.-U. (2012) · Nature Protocols · doi:10.1038/nprot.2012.119 · Cited by 992

Advanced CLARITY for rapid and high-resolution imaging of intact tissues

Tomer, R., Ye, L., Hsueh, B., & Deisseroth, K. (2014) · Nature Protocols · doi:10.1038/nprot.2014.123 · Cited by 842

CLARITY for mapping the nervous system

Chung, K., & Deisseroth, K. (2013) · Nature Methods · doi:10.1038/nmeth.2481 · Cited by 747

Selective plane illumination microscopy techniques in developmental biology

Huisken, J., & Stainier, D. Y. R. (2009) · Development · doi:10.1242/dev.022426 · Cited by 608

Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull–meninges connections

Cai, R., Pan, C., Ghasemigharagoz, A., Todorov, M. I., Förstera, B., Zhao, S., Bhatia, H. S., Parra-Damas, A., Mrowka, L., Theodorou, D., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-018-0301-3 · Cited by 470

A platform for brain-wide imaging and reconstruction of individual neurons

Economo, M. N., Clack, N. G., Lavis, L. D., Gerfen, C. R., Svoboda, K., Myers, E. W., & Chandrashekar, J. (2016) · eLife · doi:10.7554/elife.10566 · Cited by 409

LABKIT: Labeling and Segmentation Toolkit for Big Image Data

Arzt, M., Deschamps, J., Schmied, C., Pietzsch, T., Schmidt, D., Tomancak, P., Haase, R., & Jug, F. (2022) · Frontiers in Computer Science · doi:10.3389/fcomp.2022.777728 · Cited by 405

Tissue clearing of both hard and soft tissue organs with the PEGASOS method

Jing, D., Zhang, S., Luo, W., Gao, X., Men, Y., Ma, C., Liu, X., Yi, Y., Bugde, A., Zhou, B. O., et al. (2018) · Cell Research · doi:10.1038/s41422-018-0049-z · Cited by 394

The Big and the Small: Challenges of Imaging the Brain’s Circuits

Lichtman, J. W., & Denk, W. (2011) · Science · doi:10.1126/science.1209168 · Cited by 370

High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level

Gong, H., Xu, D., Yuan, J., Li, X., Guo, C., Peng, J., Li, Y., Schwarz, L. A., Li, A., Hu, B., et al. (2016) · Nature Communications · doi:10.1038/ncomms12142 · Cited by 368

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

Moffitt, J. R., Hao, J., Bambah-Mukku, D., Lu, T., Dulac, C., & Zhuang, X. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1617699113 · Cited by 308

Cellular and Molecular Probing of Intact Human Organs

Zhao, S., Todorov, M. I., Cai, R., -Maskari, R. A., Steinke, H., Kemter, E., Mai, H., Rong, Z., Warmer, M., Stanic, K., et al. (2020) · Cell · doi:10.1016/j.cell.2020.01.030 · Cited by 292

A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing

Murakami, T. C., Mano, T., Saikawa, S., Horiguchi, S. A., Shigeta, D., Baba, K., Sekiya, H., Shimizu, Y., Tanaka, K. F., Kiyonari, H., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0109-1 · Cited by 292

Design and Validation of Diffusion MRI Models of White Matter

Jelescu, I. O., & Budde, M. D. (2017) · Frontiers in Physics · doi:10.3389/fphy.2017.00061 · Cited by 240

Light-sheet microscopy in the near-infrared II window

Wang, F., Wan, H., Ma, Z., Zhong, Y., Sun, Q., Tian, Y., Qu, L., Du, H., Zhang, M., Li, L., et al. (2019) · Nature Methods · doi:10.1038/s41592-019-0398-7 · Cited by 237

Three-Dimensional Study of Alzheimer’s Disease Hallmarks Using the iDISCO Clearing Method

Liebmann, T., Renier, N., Bettayeb, K., Greengard, P., Tessier-Lavigne, M., & Flajolet, M. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.06.060 · Cited by 218

ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging

Lee, E., Choi, J., Jo, Y., Kim, J. Y., Jang, Y. J., Lee, H. M., Kim, S. Y., Lee, H.-J., Cho, K., Jung, N., et al. (2016) · Scientific Reports · doi:10.1038/srep18631 · Cited by 215

Brainbow: New Resources and Emerging Biological Applications for Multicolor Genetic Labeling and Analysis

Weissman, T. A., & Pan, Y. A. (2015) · Genetics · doi:10.1534/genetics.114.172510 · Cited by 153

Histological validation of high-resolution DTI in human post mortem tissue

Seehaus, A., Roebroeck, A., Bastiani, M., Fonseca, L., Bratzke, H., Lori, N., Vilanova, A., Goebel, R., & Galuske, R. (2015) · Frontiers in Neuroanatomy · doi:10.3389/fnana.2015.00098 · Cited by 149

Optimization of CLARITY for clearing whole-brain and other intact organs

Epp, J. R., Niibori, Y., (Liz) Hsiang, H.-L., Mercaldo, V., Deisseroth, K., Josselyn, S. A., & Frankland, P. W. (2015) · eneuro · doi:10.1523/eneuro.0022-15.2015 · Cited by 133

Enriched environment reduces glioma growth through immune and non-immune mechanisms in mice

Garofalo, S., D’Alessandro, G., Chece, G., Brau, F., Maggi, L., Rosa, A., Porzia, A., Mainiero, F., Esposito, V., Lauro, C., et al. (2015) · Nature Communications · doi:10.1038/ncomms7623 · Cited by 129

A guidebook for DISCO tissue clearing

Molbay, M., Kolabas, Z. I., Todorov, M. I., Ohn, T., & Ertürk, A. (2021) · Molecular Systems Biology · doi:10.15252/msb.20209807 · Cited by 96

Integrated brain atlas for unbiased mapping of nervous system effects following liraglutide treatment

Salinas, C. B. G., Lu, T. T.-H., Gabery, S., Marstal, K., Alanentalo, T., Mercer, A. J., Cornea, A., Conradsen, K., Hecksher-Sørensen, J., Dahl, A. B., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-28496-6 · Cited by 95

Routine Optical Clearing of 3D-Cell Cultures: Simplicity Forward

Nürnberg, E., Vitacolonna, M., Klicks, J., von Molitor, E., Cesetti, T., Keller, F., Bruch, R., Ertongur-Fauth, T., Riedel, K., Scholz, P., et al. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.00020 · Cited by 93

In vivo NIR-II structured-illumination light-sheet microscopy

Wang, F., Ma, Z., Zhong, Y., Salazar, F., Xu, C., Ren, F., Qu, L., Wu, A. M., & Dai, H. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2023888118 · Cited by 85

Whole-mouse clearing and imaging at the cellular level with vDISCO

Cai, R., Kolabas, Z. I., Pan, C., Mai, H., Zhao, S., Kaltenecker, D., Voigt, F. F., Molbay, M., Ohn, T.-L., Vincke, C., et al. (2023) · Nature Protocols · doi:10.1038/s41596-022-00788-2 · Cited by 83

Voxel-wise comparisons of cellular microstructure and diffusion-MRI in mouse hippocampus using 3D Bridging of Optically-clear histology with Neuroimaging Data (3D-BOND)

Stolp, H. B., Ball, G., So, P.-W., Tournier, J.-D., Jones, M., Thornton, C., & Edwards, A. D. (2018) · Scientific Reports · doi:10.1038/s41598-018-22295-9 · Cited by 59

Formalin-Induced Fluorescence Reveals Cell Shape and Morphology in Biological Tissue Samples

Leischner, U., Schierloh, A., Zieglgänsberger, W., & Dodt, H.-U. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010391 · Cited by 40