NeuBtracker is an open-source tracking microscope that enables concurrent neuro- and behavioral imaging in freely behaving zebrafish larvae. We used off-the shelf components to implement a mirror-based tracking system that avoids moving stages, objectives or illumination beams which may have confounding effects on behavior. This website accompanies an article about NeuBtracker in Nature Methods (publisher's link) and presents detailed blueprints of the hardware components, code for data acquisition and processing, as well as examples for the application of NeuBtracker. We hope that the information compiled in the article and on these pages can be valuable as a starting point for other laboratories to build similar devices for neurobehavioral research.

Please read the full manuscript provided by Springer's SharedIt Initiative.

NeuBtracker: Design

  • open source interrogation platform built from off-the shelf components
  • mirror-based tracking avoids moving stages, objectives or light beams to minimize confounding effects on
  • dynamically adjustable magnification for observing fluorescence signals from the entire fish or only from zoom-ins to the brain etc.
  • dynamic refocusing to compensate for different swimming depths, e.g., across developmental stages
  • compatible with custom-built swimming arenas including multiwell plates for high-throughout neurobehavioral drug screens
  • long term recordings possible for longitudinal observation of developmental stages
  • option to steer laser foci via the galvanometric mirrors to provide visual stimuli or photostimulation



NeuBtracker: Applications

Concurrent recording of neuronal activity and behavior

  • spontaneous behavior
  • response to odorants and metabolic stimuli
  • neurobehavioral screening of drugs
  • sensorimotor integration, reorientation behavior

Possible extension to multiplexed acquisition of signaling processes also within the cardiovascular, immunological and gastrointestinal systems.

Olfactory Stimulation

Swimming trajectory before and after application of an aversive odorant (top) and corresponding calcium activity in the olfactory epithelium (bottom)

Neurobehavioral Drug Screening

Dose-dependent increase in neuronal activation and transient rise in swimming activity in response to a neurostimulant

Stimulus-induced neurobehavioral effects

Neuronal and behavioral responses to repeated dark-light cycles. Calcium activity in the pineal complex (top) and concomitant changes in the swimming behavior (bottom)

Overview Videos

This is an overview video of NeuBtracker's as featured in the original publication on Nature Methods (doi: 10.1038/nmeth.4459).


Blueprints of NeuBtracker are available for Autodesk Inventor.
We provide online previews of the various configurations and features as well as the design files.