PhD Candidate in Neuroscience: Brain Architecture and Sensory Processing in the Zebrafish Forebrain

NTNU - Norwegian University of Science and Technology; Trondheim; On-site; NOK 480,000 - 560,000; Full time

Job summary

NTNU - Norwegian University of Science and Technology seeks a highly motivated PhD Candidate in Neuroscience to investigate brain architecture and sensory processing in the zebrafish forebrain. The project combines cutting-edge imaging and computational approaches to relate structure to function.

The successful candidate joins the Yaksi lab at the Kavli Institute, engaging in multidisciplinary research, international collaborations, and teaching activities while pursuing doctoral studies toward

Qualifications

• Hands-on experience with 3D electron microscopy reconstruction.
• Proficiency in Python and data analysis workflows.
• Experience with confocal microscopy and histology.
• Strong communication and collaboration skills in English.

Responsibilities

• Complete the doctoral education and obtain a doctorate.
• Carry out high-quality research within the project scope.
• Contribute to publications and science dissemination.
• Participate in the Yaksi lab group and international activities.
• Engage in conferences and research stays at foreign institutions.
• Contribute to undergraduate and master-level teaching.

Skills

3D EM reconstruction

Python programming

data analysis

neural tracing

Education

Master's degree in neuroscience

Tools

CAVEclient

CloudVolume

Neuroglancer

Blender

Job description

PhD Candidate in Neuroscience: Brain Architecture and Sensory Processing in the Zebrafish Forebrain

NTNU - Norwegian University of Science and Technology

Stillingstittel PhD in Neuroscience - Brain Architecture and Sensory Processing in the Zebrafish Forebrain

NTNU is a broad-based university with atechnical-scientific profile and a focusin professional education. The university is located in three cities with headquarters in Trondheim.

At NTNU, 9,000 employees and 43,000 students work to create knowledge for a better world.

You will find more information about working at NTNU and the application process here.

Video:

We are looking for a highly motivated PhD Candidate to join our research group and investigate the neural architecture underlying sensory processing in the zebrafish forebrain. This project will employ a powerful combination of cutting-edge imaging and computational approaches to reveal how the structural organization of brain circuits shapes sensory computation.

Are you motivated to take a step towards a doctorate and open up exciting career opportunities? As a PhD Candidate with us, you will work to achieve your doctorate, and at the same time gain valuable experience that qualifies you for a further career in higher education and research, in and outside academia.

Your immediate leader will be Professor Emre Yaksi.

This project aims to unravel how brain architecture shapes sensory processing in the zebrafish forebrain. Using zebrafish as a powerful vertebrate model organism — owing to their optical transparency, genetic tractability, and conserved vertebrate neural organization — the successful candidate will integrate multiple high-resolution imaging modalities to reconstruct neural circuits at unprecedented resolution and link structural organization to functional sensory responses.

Specifically, the project will pursue the following interconnected aims:

• 3D Electron Microscopy Reconstructions: Reconstruct and analyze large-scale, high-resolution ultrastructural maps of zebrafish forebrain circuits using 3D volume electron microscopy. Synaptic connectivity, cell type identity, and subcellular organization will be extracted using state-of-the-art segmentation and reconstruction software packages.
• Calcium Imaging: Employ two-photon calcium imaging to record population-level neural activity in the zebrafish forebrain during defined sensory stimulation paradigms. Functional response properties will be mapped onto anatomically identified circuit elements.
• Confocal Microscopy and Histology: Use confocal microscopy, immunohistochemistry, fluorescence in situ hybridization, and tissue clearing approaches to characterize cell types, molecular markers, and projection patterns in the zebrafish forebrain.
• Anatomical Reconstructions: Perform single-neuron and population-level anatomical reconstructions to map connectivity patterns and delineate the structural organization of forebrain sensory circuits.
• Data Analysis and Computational Methods: Develop and apply computational pipelines for processing large-scale imaging datasets, integrating structural and functional data, and identifying organizational principles of sensory processing circuits.

This project requires a truly multidisciplinary approach, combining experimental and computational methods to generate a mechanistic understanding of how brain structure gives rise to sensory function.

Duties of the position

• Complete the doctoral education until obtaining a doctorate
• Carry out high-quality research within the framework described above
• Contribute to academic publications and popular science dissemination
• Participate actively in the research group: the Yaksi lab at the Kavli Institute
• Participate in international activities such as conferences and/or research stays at foreign institutions
• Contribute to undergraduate and master-level teaching
• Engage in career-promoting activities (seminars, journal clubs, lab meetings)

Be prepared for changes to your work duties after employment.

Required selection criteria

• Hands-on experience with reconstructing 3D electron microscopy and associated data analytical software packages for image segmentation and neural reconstruction (e.g.,CAVEclient, CloudVolume, Neuroglancer, or equivalent).
• Hands-on experience producing 3D visualizations, renderings, or animations of reconstructed neural structures or volumetric imaging data (e.g., using Blender or comparable 3D rendering software), to support scientific communication and dissemination of the project's findings.
• Experience with Python programming, including data analysis libraries (e.g., NumPy, SciPy, etc.) and/or image processing packages. Proficiency in scripting reproducible analysis pipelines is expected.
• Practical experience with confocal microscopy and standard histological techniques, including immunohistochemistry, fluorescence labeling, and/or tissue clearing methods.
• Experience with anatomical reconstructions of neural circuits, including tracing of axonal projections, dendritic arbors, or synaptic connectivity, from either light-microscopy or electron-microscopy datasets.
• Experience with zebrafish husbandry, including routine maintenance of zebrafish colonies, breeding, and basic larval and adult handling procedures.

Excellent written and oral communication skills in English.

You must have an academically relevant background in Neuroscience, or a closely related discipline.

You must have a relevant Master's degree in neuroscience,