@conference {65385, title = {Multiplexed 3-photon microscopy for functional connectomics of mammalian brains.}, booktitle = {Multiphoton Microscopy in the Biomedical Sciences XXMultiphoton Microscopy in the Biomedical Sciences XX}, year = {2020}, month = {2020 Feb 14}, publisher = {SPIE}, organization = {SPIE}, address = {San Francisco, United States}, abstract = {

3-photon excitation enables in vivo fluorescence microscopy deep in densely labeled and highly scattering samples, while maintaining high resolution and contrast. We designed and characterized a dual-plane 3-photon microscope with temporal multiplexing and remote focusing, and performed simultaneous in vivo calcium imaging of two planes deep in the cortex of a transgenic mouse expressing GCaMP6s in nearly all excitatory neurons.

}, doi = {10.1117/12.2543232 }, url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/11244/2543232/Multiplexed-3-photon-microscopy-for-functional-connectomics-of-mammalian-brains/10.1117/12.2543232.full}, author = {Takasaki, Kevin and Tsyboulski, Dmitri A. and Waters, Jack} } @article {65241, title = {Dual-plane 3-photon microscopy with remote focusing.}, journal = {Biomedical Optics Express}, volume = {10}, year = {2019}, month = {2019 Nov 1}, pages = {5585-5599}, abstract = {

3-photon excitation enables fluorescence microscopy deep in densely labeled and highly scattering samples. To date, 3-photon excitation has been restricted to scanning a single focus, limiting the speed of volume acquisition. Here, for the first time to our knowledge, we implemented and characterized dual-plane 3-photon microscopy with temporal multiplexing and remote focusing, and performed simultaneous calcium imaging of two planes beyond 600 {\textmu}m deep in the cortex of a pan-excitatory GCaMP6s transgenic mouse with a per-plane framerate of 7 Hz and an effective 2 MHz laser repetition rate. This method is a straightforward and generalizable modification to single-focus 3PE systems, doubling the rate of volume (column) imaging with off-the-shelf components and minimal technical constraints.

}, issn = {2156-7085}, doi = {10.1364/BOE.10.005585}, author = {Takasaki, Kevin T and Tsyboulski, Dmitri and Waters, Jack} } @article {49518, title = {Visual physiology of the layer 4 cortical circuit in silico.}, journal = {PLoS Computational Biology}, volume = {14}, year = {2018}, month = {2018 Nov 12}, pages = {e1006535}, abstract = {

Despite advances in experimental techniques and accumulation of large datasets concerning the composition and properties of the cortex, quantitative modeling of cortical circuits under in-vivo-like conditions remains challenging. Here we report and publicly release a biophysically detailed circuit model of layer 4 in the mouse primary visual cortex, receiving thalamo-cortical visual inputs. The 45,000-neuron model was subjected to a battery of visual stimuli, and results were compared to published work and new in vivo experiments. Simulations reproduced a variety of observations, including effects of optogenetic perturbations. Critical to the agreement between responses in silico and in vivo were the rules of functional synaptic connectivity between neurons. Interestingly, after extreme simplification the model still performed satisfactorily on many measurements, although quantitative agreement with experiments suffered. These results emphasize the importance of functional rules of cortical wiring and enable a next generation of data-driven models of in vivo neural activity and computations.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1006535}, author = {Arkhipov, Anton and Gouwens, Nathan W and Billeh, Yazan N and Gratiy, Sergey and Iyer, Ramakrishnan and Wei, Ziqiang and Xu, Zihao and Abbasi-Asl, Reza and Berg, Jim and Buice, Michael and Cain, Nicholas and da Costa, Nuno and de Vries, Saskia and Denman, Daniel and Durand, Severine and Feng, David and Jarsky, Tim and Lecoq, Jerome and Lee, Brian and Li, Lu and Mihalas, Stefan and Ocker, Gabriel K and Olsen, Shawn R and Reid, R Clay and Soler-Llavina, Gilberto and Sorensen, Staci A and Wang, Quanxin and Waters, Jack and Scanziani, Massimo and Koch, Christof} }