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Journal Article

Pan-neuronal calcium imaging with cellular resolution in freely swimming zebrafish

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Kim, D., Kim, J., Marques, J., Hildebrand, D., Gu, W., Li, J., et al. (2017). Pan-neuronal calcium imaging with cellular resolution in freely swimming zebrafish. Nature methods, 14(11), 1107-1114. doi:10.1038/nmeth.4429.

Cite as: https://hdl.handle.net/21.11116/0000-0004-D06C-8
Calcium imaging with cellular resolution typically requires an animal to be tethered under a microscope, which substantially restricts the range of behaviors that can be studied. To expand the behavioral repertoire amenable to imaging, we have developed a tracking microscope that enables whole-brain calcium imaging with cellular resolution in freely swimming larval zebrafish. This microscope uses infrared imaging to track a target animal in a behavior arena. On the basis of the predicted trajectory of the animal, we applied optimal control theory to a motorized stage system to cancel brain motion in three dimensions. We combined this motion-cancellation system with differential illumination focal filtering, a variant of HiLo microscopy, which enabled us to image the brain of a freely swimming larval zebrafish for more than an hour. This work expands the repertoire of natural behaviors that can be studied with cellular-resolution calcium imaging to potentially include spatial navigation, social behavior, feeding and reward.