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

This is NTNU NTNU is a broad-based university with a technical-scientific profile and a focus in 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: https://www.youtube.com/watch?v=_KHQjc4ndas&t=41sAbout the position 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.

About the project The successful candidate will be part of the Yaksi lab at the Kavli Institute for Systems Neuroscience, NTNU, under the mentorship of 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, biomedical sciences, biology, or equivalent. Your degree must include a major independent project (minimum 30 ECTS) equivalent to a master’s thesis. Master students can apply, but the master's degree must be obtained and documented before starting the position in July 2027. You must have a strong and relevant academic background from your previous studies and have an average grade from your Master's degree study, or equivalent education, which is equal to B or better compared to NTNU's grading scale. If you do not have letter grades from previous studies, you must have an equally good academic foundation. If you have a weaker academic background, you may be considered if you can document that you are exceptionally suited for a PhD education, for example through relevant work experience and/or peer-reviewed academic works.

You must meet the requirements for admission to the faculty's Doctoral Programme, see Section 6-1 of the PhD regulations for more information. The appointment is to be made in accordance with NTNUs guidelines for recruitment positions for general criteria for the position.

Preferred selection criteria

• •Experience with calcium imaging (two-photon) and associated data analysis of neural population activity in zebrafish or other vertebrate models.
• •Co-authorship in a high quality peer-reviewed scientific publication or preprint. This is considered a major advantage and will be weighted strongly in the candidate assessment.
• •Excellent oral presentation skills and experience presenting research at group meetings, workshops, or international conferences.
• •Experience preparing scientific figures using Adobe Illustrator, Inkscape, or comparable graphic design software.

Personal characteristics To complete a doctoral degree (PhD), it is important that you are able to:

• Work independently and take initiative • Work in a structured way, set goals, and make plans to achieve them • Present and discuss your research with other professionals • Get involved and contribute constructively with feedback • Work constructively under pressure or in the face of adversity • Show curiosity and a strong motivation for the subject • Analyze data, assess different perspectives, and draw well-founded conclusions • Be flexible and open to adjusting the plan for the project as needed. Emphasis will be placed on personal qualities.

We offer

• •An exciting research position in a world-leading neuroscience institute with an importan