J.B. Treweek , A. Beres, N. Johnson, and A. Greenbaum (2021) Phenotyping Intact Mouse Bones Using Bone CLARITY. In: Hilton M.J. (eds) Skeletal Development and Repair. Methods in Molecular Biology, vol 2230. Humana, New York, NY.
A. Moatti, Y. Cai, C. Li, T. Sattler, L. Edwards, J. Piedrahita, F. S. Ligler, and A. Greenbaum ,"Three-dimensional imaging of intact porcine cochlea using tissue clearing and custom-built light-sheet microscopy," Biomed. Opt. Express 11(11), 6181–6196 (2020).
S. Ravindra Kumar, T. F. Miles, X. Chen, D. Brown, T. Dobreva, Q. Huang, X. Ding, Y. Luo, P. H. Einarsson, A. Greenbaum, M. J. Jang, B. E. Deverman, and V. Gradinaru, "Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types," Nature Methods 17(5), 541–550 (2020).
P. S. Rajendran, R. C. Challis, C. C. Fowlkes, P. Hanna, J. D. Tompkins, M. C. Jordan, S. Hiyari, B. Gabris-Weber, A. Greenbaum, K. Y. Chan, B. E. Deverman, H. Münzberg, J. L. Ardell, G. Salama, V. Gradinaru, K. Shivkumar, “Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies,” Nature Communications, 10, 1944 (2019).
A. Greenbaum, M. J. Jang, C. Challis and V. Gradinaru, “Q&A: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology?” BMC Biology, 15, 87 (2017).
A. Greenbaum*, K. Chan*, T. Dobreva, D. Brown, D. H. Balani, R. Boyce, H. M. Kronenberg, H. J. McBride and V. Gradinaru, “Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow,” Science Translational Medicine, 9, eaah6518 (2017). (*) Joint first author.
K. Chan, M. J. Jang, B. B. Yoo, A. Greenbaum, N. Ravi, W.-L. Wu, S. K. Mazmanian, B. E. Deverman, and V. Gradinaru, “Engineered adeno- associated viruses for efficient and noninvasive gene delivery throughout the central and peripheral nervous systems,” Nature Neuroscience, 20, 1172-1179 (2017).
J. R. Cho, J. B. Treweek, J. E. Robinson, C. Xiao, L. R. Bremner, A. Greenbaum and V. Gradinaru, “Dorsal Raphe Dopamine Neurons Modulate Arousal and Promote Waking by Salient Stimuli,” Neuron, 94, 1205-1219 (2017).
A. Feizi, Y. Zhang, A. Greenbaum, A. Guziak, M. Luong, R.Y. Chan, B. Berg, H. Ozkan, W. Luo, M. Wu, Y. Wu, and A. Ozcan,” Rapid, portable and cost-effective yeast cell viability and concentration analysis using lensfree on-chip microscopy and machine learning,” Lab Chip, 16, 4350-4358 (2016).
S. Shah*, E. Lubeck*, M. Schwarzkopf*, T. He*, A. Greenbaum*, C. H. Sohn, A. Lignell, H. M. T. Choi, V. Gradinaru, N. A. Pierce, and L. Cai, “Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing,” Development, 143, 2862-2867 (2016). (*) Joint first author.
J. B. Treweek, B. Yang, N. Flytzanis, K. Chan, B. E. Deverman, A. Greenbaum, A. Lignell, C. Xiao, L. Cai, M. S. Ladinsky, P. Bjorkman, C. C. Fowlkes, and V. Gradinaru, “Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping,” Nature Protocols, 10, 1860-1896 (2015).
W. Luo, F. Shabbir, C. Gong, C. Gulec, J. Pigeon, J. Shaw, A. Greenbaum, S. Tochitsky, C. Joshi, and A. Ozcan, “High throughput on-chip analysis of high-energy charged particle tracks using lensfree imaging,” APL 106, 151107 (2015).
E. McLeod, T.U. Dincer, M. Veli, Y.N. Ertas, C. Nguyen, W. Luo, A. Greenbaum, A. Feizi, and A. Ozcan, “High-throughput and label-free single nanoparticle sizing based on time-resolved on-chip microscopy,” ACS Nano 9, 3265-3273 (2015).
W. Luo*, A. Greenbaum*, Y. Zhang, and A. Ozcan, “Synthetic aperture based on-chip microscopy,” Light: Science & Applications, 4, e261 (2015). (*) Joint first author.
A. Greenbaum, Y. Zhang, A. Feizi, P. L. Chung, W. Luo, S. R. Kandukuri and A. Ozcan, “Wide-field computational imaging of pathology slides using lens-free on-chip microscopy,” Science Translational Medicine 6, 267ra175 (2014).
A. Greenbaum, A. Feizi, N. Akbari, W. Luo, and A. Ozcan, “Field portable pixel super-resolution colour microscope,” PLoS ONE 8, e76475 (2013).
A. Greenbaum, A. Feizi, N. Akbari, and A. Ozcan, “Wide-field computational color imaging using pixel super-resolved on-chip microscopy,” Opt. Express 21, 12469-12483 (2013).
A. Greenbaum, W. Luo, B. Khademhosseinieh, T. W. Su, A.F. Coskun, and A. Ozcan, “Increased space-bandwidth product in pixel super-resolved lensfree on-chip microscopy,” Sci. Rep. 3, 1717 (2013).
E. McLeod, W. Luo, O. Mudanyali, A. Greenbaum, and A. Ozcan, “Toward giga-pixel nanoscopy on a chip: a computational wide-field look at the nano-scale without the use of lenses,” Lab Chip 13, 2028-2035 (2013).
O. Mudanyali, E. McLeod, W. Luo, A. Greenbaum, A. Coskun, Y. Hennequin, C. Allier, and A. Ozcan, “Wide-field optical detection of nano-particles using on-chip microscopy and self-assembled nano-lenses,” Nature Photonics, 7, 247–254 (2013).
H. Zhu, S. O. Isikman, O. Mudanyali, A. Greenbaum and A. Ozcan, “Optical Imaging techniques for point-of-care diagnostics,” Lab Chip 13, 51-67 (2013).
J. Weidling, S.O. Isikman, A. Greenbaum, A. Ozcan, E. Botvinick, “Lens-free computational imaging of capillary morphogenesis within three-dimensional substrates,” J. Biomed. Opt. 17, 126018-126018 (2012).
S. O. Isikman, A. Greenbaum*, W. Luo, A. Coskun, and A. Ozcan, " Giga-pixel lensfree holographic microscopy and tomography using color image sensors," PLoS ONE 7, e45044 (2012). (*) Joint first author.
A. Greenbaum, W. Luo, T-W. Su, Z. Gorocs, L. Xue, S.O. Isikman, A.F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nature Methods 9, 889-895 (2012).
A. Greenbaum, and A. Ozcan, “Maskless imaging of dense samples using pixel super-resolution based multi-height lensfree on-chip microscopy,” Opt. Express 20, 3129-3143 (2012).
A. Greenbaum, U. Sikora, and A. Ozcan, “Field-portable wide-field microscopy of dense samples using multi-height pixel super-resolution based lensfree imaging,” Lab Chip 12, 1242-1245 (2012).
S. O. Isikman, A. Greenbaum, M. Lee, W. Bishara, O. Mudanyali, T. W. Su and A. Ozcan, "Lensfree computational microscopy tools for cell and tissue imaging at the point-of-care and in low-resource settings," Anal. Cell. Pathology 36, 1-19 (2012).
G. Biener, A. Greenbaum, S.O. Isikman, K. Lee, D. Tseng and A. Ozcan, “Combined reflection and transmission microscope for telemedicine applications in field settings,” Lab Chip 11, 2738-2743 (2011).
A. Greenbaum, S. Anava, A. Ayali, M. Shein, M. David-Pur, E. Ben-Jacob and Y. Hanein. “One to one neuron-electrode interfacing,” J. Neurosci. Meth. 182, 219-224 (2009).
R. Sorkin, A. Greenbaum, M. David-Pur, S. Anava, A. Ayali, E. Ben-Jacob, and Yael Hanein, “Process entanglement as a neuronal adhesion mechanism,” Nanotechnology 20, 015101 (2009).
S. Anava, A. Greenbaum, E. Ben Jacob, Y. Hanein and A. Ayali, “The regulative role of neurite mechanical tension in network development,” Biophys. J. 96, 1661-1670 (2009).
M. Shein, A. Greenbaum, T. Gabay, R. Sorkin, M. David-Pur, E. Ben-Jacob, and Y. Hanein, “Engineered neuronal circuits shaped and interfaced with carbon nanotube microelectrode arrays,” Biomed. Microdevices 11, 495-501 (2009).