Publications and Techniques


Text2Brain: Synthesis of Brain Activation Maps from Free-Form Text Query G. H. Ngo, M. Nguyen, N. F. Chen, and M. R. Sabuncu In M. de Bruijne, P. C. Cattin, S. Cotin, N. Padoy, S. Speidel, Y. Zheng, & C. Essert (Eds.), Medical Image Computing and Computer Assisted Intervention – MICCAI 2021: 24th International Conference, Strasbourg, France, September 27 – October 1, 2021, Proceedings, Part VII (Vol. 12907, pp. 605–614). Cham: Springer International Publishing (2021).

Heritability and interindividual variability of regional structure-function coupling


Z. Gu, K. W. Jamison, M. R. Sabuncu, A. Kuceyeski Nature Communications 12, 2021. DOI: 10.1038/s41467-021-25184-4
“Closed-loop wavefront sensing and correction in the mouse brain with computed optical coherence microscopy” Siyang Lu, Fei Xia, Xusan Yang, Meiqi Wu, Laurie A. Bizimana, Chris Xu, and Steven G. Adie

Biomedical Optics Express, Vol. 12, Number 8. August , 2021. DOI:


“Multicolor three-photon fluorescence imaging with single-wavelength excitation deep in mouse brain” Yusaku Hontani, Fei Xia, and Chris Xu

Science Advances, Vol. 7, Number 12. March 17, 2021. DOI:


“Three-photon neuronal imaging in deep mouse brain” Tianyu Wang and Chris Xu

Optica, Vol. 7, Issue 8, pp. 947-960 DOI:


“Deep three-photon imaging of the brain in intact adult zebrafish” Dawnis M. Chow, David Sinefeld, Kristine E. Kolkman, Dimitre G. Ouzounov, Najva Akbari, Rose Tatarsky, Andrew Bass, Chris Xu, and Joseph R. Fetcho Nature Methods, April 27, 2020, 1548-7091, 1548-7105 DOI: 10.1038/s41592-020-0819-7
“Surgical preparations, labeling strategies, and optical techniques for cell-resolved, in vivo imaging in the mouse spinal cord” Yu-Ting Cheng, Kawasi M. Lett, and Chris B. Schaffer Experimental Neurology, August 2019, Volume 318, 192-204 DOI: 10.1016/j.expneurol.2019.05.010
“Simultaneous Two- and Three-photon Imaging of Multilayer Neural Activities with Remote Focusing” Aaron T. Mok, Tianyu Wang, Fei Xia, Chunyan Wu, and Chris Xu. Conference on Lasers and Electro-Optics, OSA Technical Digest (Optical Society of America, 2019), paper AM1I.5. DOI: 10.1364/CLEO_AT.2019.AM1I.5
“Quantitative analysis of 1300-nm three-photon calcium imaging in the mouse brain” Tianyu Wang, Chunyan Wu, Dimitre G Ouzounov, Wenchao Gu, Fei Xia, Minsu Kim, Xusan Yang, Melissa R Warden, and Chris Xu eLife 2020;9:e53205. DOI: 10.7554/eLife.53205
“An adaptive excitation source for high-speed multiphoton microscopy” Bo Li, Chunyan Wu, Mengran Wang, Kriti Charan, and Chris Xu Nature Methods 17, 163–166 (2020). DOI: 10.1038/s41592-019-0663-9
“Deep convolutional neural networks for segmenting 3D in vivo multi photon images of vasculature in Alzheimer disease mouse models” Mohammad Haft-Javaherian, Linjing Fang, Victorian Muse, Chris B. Schaffer, Nozomi Nishimura, Mert R. Sabuncu PLOS ONE, 14(3), e0213539, 2019.
“Ensemble learning with 3D convolutional neural networks for functional connectome-based prediction” Meenakshi Khosla, Keith Jamison, Amy Kuceyeski, Mert R. Sabuncu NeuroImage, 199, 651-662,  2019.
“GCaMP6 ΔF/F dependence on the excitation wavelength in 3-photon and 2-photon microscopy of mouse brain activity” Dimitre G. Ouzounov, Tianyu Wang, Chunyan Wu, Chris Xu Biomedical Opt. Express, 10(7), 3343-3352, 2019.
“A Bayesian Disease Progression Model for Clinical Trajectories” Yingying Zhu, Mert R. Sabuncu Graphs in Biomedical Image Analysis and Integrating Medical Imaging and Non-Imaging Modalities (pp. 57-65). Springer International Publishing, 2019.
“Impact of the emission wavelengths on in vivo
multiphoton imaging of mouse brains”
Mengran Wang, Minsu Kim, Fei Xia, and Chris Xu  Biomed. Opt. Express 10, 1905-1918, 2019.
 “Comparison of emission wavelengths for in vivo deep imaging of mouse brain”  Mengran Wang, Minsu Kim, Fei Xia, and Chris Xu Proc. SPIE 10882, Multiphoton Microscopy in the Biomedical Sciences XIX, 108822I, 2019.
“Three-photon imaging of mouse brain structure and function through the intact skull” Tianyu Wang, Dimitre G. Ouzounov, Chunyan Wu, Nicholas G. Horton, Bin Zhang, Cheng-Hsun Wu, Yanping Zhang, Mark J. Schnitzer, and Chris Xu Nature Methods, 1548-7105, 2018.
“Comparing the effective attenuation lengths for long wavelength in vivo imaging of the mouse brain” Mengran Wang, Chunyan Wu, David Sinefeld, Bo Li, Fei Xia, and Chris Xu Biomed. Opt. Express, 9, 3534-3543, 2018.
“An adaptive excitation source for multiphoton imaging” Bo Li, Mengran Wang, Chunyan Wu, Kriti Charan, and Chris Xu CLEO Postdeadline Papers Session III, OSA Technical Digest, paper JTh5C.5, 2018.
“Comparison of excitation wavelengths for in vivo deep imaging of mouse brain” Mengran Wang, Chunyan Wu, Bo Li, Fei Via, David Sinefeld, and Chris Xu Proc. SPIE 10498, Multiphoton Microscopy in the Biomedical Sciences XVIII, 104982A, 2018.
“In vivo three-photon imaging of deep mouse cerebellum” Mengran Wang, Tianyu Wang, Chunyan Wu, Bo Li, Dimitre G. Ouzounov, David Sinefeld, Akash Guru, Hyung-Song Nam, Mario R. Capecchi, Melissa R. Warden, and Chris Xu Proc. SPIE 10498, Multiphoton Microscopy in the Biomedical Sciences XVIII, 1049816, 2018.
“Fiber-based, tunable repetition rate source for deep tissue two-photon fluorescence microscopy” Kriti Charan, Bo Li, Mengran Wang, Charles P. Lin, and Chris Xu Biomedical Optics Express, 9, 2304-2311, 2018.
“Generalized Cross Entropy Loss for Training Deep Neural Networks with Noisy Labels” Zhilu Zhang and Mert R. Sabuncu 32nd Conference on Neural Information Processing Systems (NeurIPS 2018), Montréal, Canada, 2018.
“Investigation of the long wavelength limit of soliton self-frequency shift in a silica fiber” Bo Li, Mengran Wang, Kriti Charan, Ming-jun Li, and Chris Xu Opt. Express 26, 19637-19647, 2018.