NeuroNex: Cornell

* Experts from physics, engineering and biology will work together to develop a suite of optical imaging tools that will overcome current barriers in the depth, breath and speed of imaging to enable the structure and activity of neurons throughout living brains of intact animals across a range of species to be mapped during the execution of complex behaviors
* Optical technologies for large scale, noninvasive recording of neural activity
* The goal of the Cornell NeuroNex Technology Hub is to rapidly introduce technology advancements to the neuroscience community
* DeepVess is a 3D convolutional neural network (CNN) segmentation method with essential pre- and post-processing steps, to fully automate the vascular segmentation of 3D in-vivo multi-photon microscopy (MPM images of murine brain vasculature using TensorFlow

* Deep imaging of intact brains – Multiphoton microscopy, invented at Cornell, has allowed neuroscientists to record the activities of individual neurons up to approximately 1 millimeter deep into a mouse brain
* Imaging of large and multiple neural regions – Using a combination of two- and three-photon microscopy, the hub will develop a new tool to simultaneously observe neurons in different regions of the mouse brain and the spinal cord
* Faster imaging for volumetric recording – By leveraging prior knowledge of the sample, optimum laser exposure will be used to record the activities from a large number of neurons
* Cornell scientists have developed a new technique for imaging a zebrafish’s brain at all stages of its development, which could have implications for the study of human brain disorders, including autism.
* in vivo three-photon imaging of mouse brain
* Deep three-photon imaging of the brain in intact adult zebrafish
* Quantitative analysis of 1300-nm three-photon calcium imaging in the mouse brain

* We developed an adaptive femtosecond excitation source that only illuminates the region of interest, which leads to a 30-fold reduction in the power requirement for two- or three-photon imaging of brain activity in awake mice for improved high-speed longitudinal neuroimaging
* We demonstrated three-photon imaging of vasculature through the adult mouse skull at >500-μm depth, as well as GCaMP6s calcium imaging over weeks in cortical layers 2/3 and 4 in awake mice, with 8.5 frames per second and a field of view spanning hundreds of micrometers
* We showed that three-photon (3P) imaging through the head of intact adult zebrafish allows structural and functional imaging at cellular resolution throughout the telencephalon and deep into the cerebellum and optic tectum

* Mouse brain, spinal cord, spleen, lymph nodes; fish, fly, etc

* Deep imaging; Adaptic excitation source for fast imaging

* Relatively expensive laser source

* Tianyu Wang and Chris Xu, “”Three-photon neuronal imaging in deep mouse brain,”” Optica 7, 947-960 (2020)

* Li, B., Wu, C., Wang, M. et al. An adaptive excitation source for high-speed multiphoton microscopy. Nat Methods 17, 163–166 (2020). https://doi-org.proxy.library.cornell.edu/10.1038/s41592-019-0663-9

* Chow, D.M., Sinefeld, D., Kolkman, K.E. et al. Deep three-photon imaging of the brain in intact adult zebrafish. Nat Methods 17, 605–608 (2020). https://doi-org.proxy.library.cornell.edu/10.1038/s41592-020-0819-7

* Wang T, Wu C, Ouzounov DG, Gu W, Xia F, Kim M, Yang X, Warden MR, Xu C. Quantitative analysis of 1300-nm three-photon calcium imaging in the mouse brain. Elife. 2020 Jan 30;9:e53205. doi: 10.7554/eLife.53205. PMID: 31999253; PMCID: PMC7028383

* Wang, T., Ouzounov, D.G., Wu, C. et al. Three-photon imaging of mouse brain structure and function through the intact skull. Nat Methods 15, 789–792 (2018). https://doi-org.proxy.library.cornell.edu/10.1038/s41592-018-0115-y

* Ouzounov, D., Wang, T., Wang, M. et al. In vivo three-photon imaging of activity of GCaMP6-labeled neurons deep in intact mouse brain. Nat Methods 14, 388–390 (2017). https://doi-org.proxy.library.cornell.edu/10.1038/nmeth.4183

* Horton, N., Wang, K., Kobat, D. et al. In vivo three-photon microscopy of subcortical structures within an intact mouse brain. Nature Photon 7, 205–209 (2013). https://doi-org.proxy.library.cornell.edu/10.1038/nphoton.2012.336

* Howard, S., Straub, A., Horton, N. et al. Frequency-multiplexed in vivo multiphoton phosphorescence lifetime microscopy. Nature Photon 7, 33–37 (2013) https://doi-org.proxy.library.cornell.edu/10.1038/nphoton.2012.307

* https://neuronex.cornell.edu

* https://neuronex.org/projects/9

* Haft-Javaherian et al. 2019, Deep convolutional neural networks for segmenting 3D in vivo multiphoton images of vasculature in Alzheimer disease mouse models, PLoS ONE 14: e0213539

* https://neuronex.cornell.edu/publications-and-techniques/

* https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0213539

* https://neuronex.cornell.edu/resources/

* https://neuronex.org/projects/9
* https://neuronex.cornell.edu/conference/
* https://www.nsf.gov/news/news_summ.jsp?cntn_id=242652

* https://neuronex.cornell.edu/helpline/

* https://neuronex.cornell.edu/deepvess-data-github/