All optical decoding of whole brain neural circuitry in zebrafish

The Naumann lab in the Department of Neurobiology at Duke University uses cutting-edge behavioral analysis and imaging technologies to study behavior and brain-scale neural circuit function in the larval zebrafish. We are interested in solving how the entire brain dynamically represents information. For this we use translucent, transgenic zebrafish which express genetically encoded activity sensors (e.g., calcium sensors like GCaMP7) in all or subsets of their neurons. Because zebrafish brains are tiny (in comparison to large mammalian brains), we can use advanced microscopy techniques to “see” their brain activity. Using high-resolution light-sheet and two-photon microscopy, we measure the activity of thousands of neurons while presenting the fish with visual stimuli, such as patterns of moving dots to understand how the brain of the zebrafish utilizes this information to make decisions about where to swim next. With these techniques, we can “read” the activity of each neuron, but we are also using light sculpting of laser light to optogenetically switch neurons on and off, which provides a method of “writing” neural activity in a living vertebrate system. Using this approach, we are also now trying to understand how sensory cells in the gut communicate with the brain. We are looking for ambitious, independent thinkers from diverse backgrounds with plans to apply to competitive PhD programs. If you join, you will be directly involved in doing research such as collecting data, perform analysis, and data visualization and will receive mentoring and ample opportunities to experience what it means to work in a basic research environment. Currently, we are looking for (1) students with interests in Biomedical engineering to help build and or optimize our microscopes and (2) students interested in data analysis work aiming to apply modern machine-learning techniques towards microscopy image analysis. Interested students can participate in either or both projects. The latter project will develop pipelines for image restoration, denoising, and multi-image alignments. Additionally, these techniques will be applied towards the construction of an image annotation platform which will be leveraged to track cells across time and space in 5-D imaging volumes. This will be
a great opportunity to learn programming and machine-learning skills in the Python programming language. Please contact the Principal Investigator and send your CV, a short introduction about yourself and your interest in neuroscience. 

Name of research group, project, or lab
Naumann lab
What is the context and setting for this research?

This is a young, basic science lab in the Department of Neurobiology. You will be part of a basic research team.

Representative publication
Logistics Information:
Project categories
Biological Sciences
Biomedical Engineering
Computer Science
Data Science Biology
Student ranks applicable
Hours per week
Paid - Work-Study Required
Unpaid - Ind. Study Credit
Number of openings
Techniques learned

Two-photon and light-sheet microscopy, fluorescence-based neural activity imaging, zebrafish neurobiology, holography, optogenetics, experimental design, data organization, management, and data visualization



This project will use a Mentor-Student contract.
Contact Information:
Eva Naumann
Assistant Professor
Name of project director or principal investigator
Eva Naumann
Email address of project director or principal investigator
2 sp. | 3 appl.
Hours per week
5-7 (+1)
Project categories
Data Science Biology (+3)
Biological SciencesBiomedical EngineeringComputer ScienceData Science Biology