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Chettih, Selmaan

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Chettih

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Selmaan

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Chettih, Selmaan
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    Geometric Deep Learning Enables 3D Kinematic Profiling Across Species and Environments
    (Springer Science and Business Media LLC, 2021-04-19) Dunn, Timothy; Marshall, Jesse; Severson, Kyle S.; Aldarondo, Diego; Hildebrand, David; Chettih, Selmaan; Wang, William; Gellis, Amanda; Carlson, David E.; Aronov, Dmitriy; Freiwald, Winrich; Wang, Fan; Ölveczky, Bence P.
    Comprehensive descriptions of animal behavior require precise measurements of 3D whole-body movements. Although 2D approaches can track visible landmarks in restrictive environments, performance drops significantly in freely moving animals, where occlusions and appearance changes are ubiquitous. To enable robust 3D tracking, we designed DANNCE, a method using projective geometry to construct inputs to a convolutional neural network that leverages learned 3D geometric reasoning to track anatomical landmarks across species and behaviors. We trained and benchmarked DANNCE using a new 7-million frame dataset relating color videos and rodent 3D poses. In rats and mice, DANNCE robustly tracked dozens of landmarks on the head, trunk, and limbs of freely moving animals in naturalistic settings, achieving over an order of magnitude better accuracy than prior techniques. We extend DANNCE to rat pups, marmosets, and chickadees, and demonstrate a novel ability to quantitatively profile behavioral lineage over development. DANNCE offers unprecedented analytical access to animal behavior across species and environments.
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    Silk Fibroin Films Facilitate Single-Step Targeted Expression of Optogenetic Proteins
    (2018) Jackman, Skyler L.; Chen, Christopher; Chettih, Selmaan; Neufeld, Shay Q.; Drew, Iain R.; Agba, Chimuanya K.; Flaquer, Isabella; Stefano, Alexis; Kennedy, Thomas J.; Belinsky, Justine E.; Roberston, Keiramarie; Beron, Celia; Sabatini, Bernardo; Harvey, Christopher; Regehr, Wade
    SUMMARY Optical methods of interrogating neural circuits have emerged as powerful tools for understanding how the brain drives behaviors. Optogenetic proteins are widely used to control neuronal activity, while genetically encoded fluorescent reporters are used to monitor activity. These proteins are often expressed by injecting viruses, which frequently leads to inconsistent experiments due to misalignment of expression and optical components. Here, we describe how silk fibroin films simplify optogenetic experiments by providing targeted delivery of viruses. Films composed of silk fibroin and virus are applied to the surface of implantable optical components. After surgery, silk releases the virus to transduce nearby cells and provide localized expression around optical fibers and endoscopes. Silk films can also be used to express genetically encoded sensors in large cortical regions by using cranial windows coated with a silk/virus mixture. The ease of use and improved performance provided by silk make this a promising approach for optogenetic studies.