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Automatically tracking neurons in a moving and deforming brain

Fig 2

Input to the pipeline.

(A) Example images from all four video feeds from our imaging system. Both scale bars are 100μm. Fluorescent images are shown with false coloring. (B)A schematic illustrating the timings from all the devices that run in open loop in our imaging setup. The camera that collects high magnification images captures at 200Hz. The two low magnification images capture at 60Hz, and the focal plane moves up and down in a 3 Hz triangle wave. The cameras are synchronized post-hoc using light flashes and each image is assigned a timestamp on a common timeline.

Fig 2