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

Ntnu; Trondheim; Hybrid; NOK 522,000 - 638,000; Full time

Benefits offered by this job

Mentor programme

Public pension plan (SPK)

Open and inclusive working environment

Job summary

NTNU is recruiting a PhD Candidate in Neuroscience to investigate brain architecture and sensory processing in the zebrafish forebrain. The project combines high-resolution imaging and computational methods to link structure and function.

You will work closely with the Yaksi lab at the Kavli Institute and contribute to publications and teaching. The successful candidate will use 3D EM, calcium imaging, confocal methods, and computational pipelines to map neural circuits and functional responses

Qualifications

• Hands-on experience with 3D EM data analysis software (CAVEclient, CloudVolume, Neuroglancer or equivalent).
• Experience producing 3D visualizations of neural structures (Blender or similar).
• Proficiency in Python with data analysis libraries and reproducible pipelines.
• Experience with confocal microscopy, immunohistochemistry, fluorescence labeling, or tissue clearing.
• Experience with anatomical reconstructions of neural circuits from imaging data.
• Zebrafish husbandry and colony maintenance experience.
• Excellent written and spoken English.
• Academic background in Neuroscience; Master’s degree with independent project (30 ECTS).
• Experience with calcium imaging and data analysis in zebrafish or vertebrates.
• Co-authorship in peer-reviewed publications is advantageous.
• Excellent oral presentation skills and scientific figure preparation experience.

Responsibilities

• Complete the doctoral education and obtain a PhD.
• Carry out high-quality research as described in the project aims.
• Contribute to publications and science dissemination.
• Participate in the Yaksi lab at the Kavli Institute.
• Attend international conferences and research stays.
• Contribute to undergraduate and master-level teaching.
• Engage in career-promoting activities and lab meetings.

Skills

3D EM reconstruction

3D visualization

Python programming

Confocal microscopy

Anatomical reconstructions

Zebrafish husbandry

Calcium imaging

Publications experience

Oral presentation

Adobe Illustrator

Education

Master's degree in neuroscience

Master's thesis (30 ECTS)

Tools

Blender

3D reconstruction tools

Job description

The Kavli Institute for Systems Neuroscience is recruiting a

PhD Candidate 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.

About 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.

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.

• 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 important mission in society
• Developing tasks in a strong and international scientific environment
• Career guidance and follow-up throughout the PhD period
• Open and inclusive working environment with committed and collaborative colleagues
• Working capital to implement the project, including access to state-of-the-art imaging infrastructure
• Mentor programme as a new employee at NTNU
• As a public employee, favorable benefits as a member of the Norwegian Public Service Pension Fund (SPK)

We strive to attract employees with different skills, life experiences and perspectives to contribute to even better problem solving of our societal mission in research and education.

Salary and conditions

In the position of PhD Candidate, code 1017, your gross salary will normally be NOK 580 000,- per annum depending on qualifications and seniority. A 2% statutory contribution to the State Pension Fund is deducted from the salary.

The employment period is three years for the doctoral work in addition to four months of career promotion work. (A minimum of three work years of the total term period must be dedicated to doctoral work.)

For employment as a PhD Candidate, it is a prerequisite that you gain admission to the PhD programme within three months of your employment contract start date, and that you participate in an organized doctoral programme through out the period of employment.

As an employee at NTNU, it is important that you keep yourself up to date with academic and organizational changes and adapt to them.

For the necessary professional and social interaction, it is a prerequisite that you are physically present and available to the institution on a daily basis.

The appointment is carried out in accordance with the principles of the State Employees Act , and Export control (legislation that regulates the export of knowledge, technology and services). Candidates who, after assessment of the application and attachments, are considered to bein conflict with the criteria in the latter act, will not be able to be employed.

If you have any questions about the position, please contact professor Emre Yaksi, email: [e-mail]

If you have any questions about the recruitment process, please contact HR advisor Camilla Perrin Wenaas, [e-mail]

The city of Trondheim is a modern European city with a rich cultural scene. Trondheim is the tech capital of Norway with a population of 200,000.The Norwegian welfare state, including healthcare, schools, kindergartens and overall equality, is probably the best of its kind in the world. Professional subsidized day-care for children is easily available. Furthermore, Trondheim offers great opportunities for education (including international schools) and possibilities to enjoy nature, culture and family life and has low crime rates and clean air quality.

NTNU - knowledge for a better world

NTNU - knowledge for a better world The Norwegian University of Science and Technology (NTNU) creates knowledge for a better world and solutions that can change everyday life. The Kavli Institute for Systems Neuroscience is part of the Faculty of Medicine and Health Sciences at NTNU. It was established as a Centre of Excellence in 2002 and designated as a Kavli Foundation Institute in 2007. The institute’s goal is to be world-leading within the field of systems neuroscience and to understand how brain circuits give rise rice to cognition, behavior, and mental function in the brain. This is achieved by integrating cutting-edge technologies with computational and translational approaches. In 2014, the Nobel Prize in Physiology or Medicine was awarded to two of the Institute’s professors, Edvard Moser and May-Britt Moser. The Institute is responsible for an international master's programme and is affiliated with a doctoral programme in medicine. Through our widespread network of international collaboration, we offer unique career opportunities The Institute’s slogan is: Excellent science, happy people, happy animals, and diversity.