Evoking and tracking zebrafish eye movement in multiple larvae with ZebEyeTrack

The design of modern scientific experiments requires the control and monitoring of many different data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for the acquisition and online processing of data streams. We describe Bonsai's core principles and architecture and demonstrate how it allows for the rapid and flexible prototyping of integrated experimental designs in neuroscience. We specifically highlight some applications that require the combination of many different hardware and software components, including video tracking of behavior, electrophysiology and closed-loop control of stimulation.

We studied the development and maturation of the visual system by determining when zebrafish begin to see and to move their eyes. This information was correlated with the time courses of the development of the retina, the retinofugal projection, the retinal image, and the extraocular muscles, to obtain an integrated picture of early visual development. Two visual behaviors were monitored over 48-96 hr postfertilization (hpf). The startle response (body twitch) was evoked by an abrupt decrease in light intensity. The optokinetic response (tracking eye movements) was evoked by rotation of a striped drum. Visually evoked startle developed over 68-79 hpf, more than 20 hr after the onset of a touch-evoked startle. It was not seen in eyeless fish, excluding a role for nonretinal light senses. Tracking eye movements developed over 73-80 hpf. They were always in the direction of drum rotation, even when the fish had been light deprived from blastula stage, ruling out a "trial and error" period of learning to track the drum. The image formed by the ocular lens was examined in intact fish made transparent by suppressing the formation of melanin. The eye was initially far sighted and gradually improved, so that by 72 hpf the image plane coincided with the photoreceptor layer. The extraocular muscles assumed their adult configuration between 66 and 72 hpf. Thus, the retinal image and functional extraocular muscles appeared nearly simultaneously with the onset of tracking eye movements and probably represent the last events in the construction of this behavior.

We examined optokinetic and optomotor responses of 450 zebrafish mutants, which were isolated previously based on defects in organ formation, tissue patterning, pigmentation, axon guidance, or other visible phenotypes. These strains carry single point mutations in >400 essential loci. We asked which fraction of the mutants develop blindness or other types of impairments specific to the visual system. Twelve mutants failed to respond in either one or both of our assays. Subsequent histological and electroretinographic analysis revealed unique deficits at various stages of the visual pathway, including lens degeneration (bumper), melanin deficiency (sandy), lack of ganglion cells (lakritz), ipsilateral misrouting of axons (belladonna), optic-nerve disorganization (grumpy and sleepy), inner nuclear layer or outer plexiform layer malfunction (noir, dropje, and possibly steifftier), and disruption of retinotectal impulse activity (macho and blumenkohl). Surprisingly, mutants with abnormally large or small eyes or severe wiring defects frequently exhibit no discernible behavioral deficits. In addition, we identified 13 blind mutants that display outer-retina dystrophy, making this syndrome the single-most common cause of inherited blindness in zebrafish. Our screen showed that a significant fraction (approximately 5%) of the essential loci also participate in visual functions but did not reveal any systematic genetic linkage to particular morphological traits. The mutations uncovered by our behavioral assays provide distinct entry points for the study of visual pathways and set the stage for a genetic dissection of vertebrate vision.