PhD Position - High-Fidelity Multi-Instance Modeling of Living Symbioses: 3D+t Reconstruction o[...]

Forschungszentrum Jülich; Jülich; On-site; EUR 38,000 - 46,000; Full time

Benefits offered by this job

30 days of annual leave

Flexible working arrangements

Comprehensive training program

Job summary

A leading research center is seeking a PhD student in machine learning to develop 3D image reconstruction methods in cell microscopy. Candidates should possess an excellent Master's degree in engineering, computer science, or mathematics, along with strong programming skills in Python and C++. The role involves working in a diverse team, presenting research at conferences, and offers outstanding scientific infrastructure with flexibility for remote work and mentoring opportunities.

Qualifications

• Excellent Master's degree required.
• Solid mathematical and physics background.
• Very good programming skills in Python and C++.
• Excellent cooperation and communication skills are necessary.
• Very good English proficiency is required.

Responsibilities

• Develop 3D+t image reconstruction methods.
• Investigate segmentation for endosymbionts.
• Implement, train, and test machine-learning solutions.
• Work in an interdisciplinary team.
• Present work at international conferences.

Skills

Programming (Python, C++)

Analytical skills

Communication skills

Team collaboration

Education

Master's degree in engineering, computer science or mathematics

Tools

Linux

Windows

Job description

You want to make an impact by connecting high-throughput cell microscopy with machine learning for 3D image reconstruction? This is the position for you! The Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) provides an interdisciplinary environment for educating the next generation of data scientists in close contact to domain‑specific knowledge and research. All three domains – life & medical sciences, earth sciences, and energy systems/materials – are characterized by the generation of huge heterogeneously structured data sets, which have to be evaluated in order to obtain a holistic understanding of very complex systems. Visit HDS-LEE at: https://www.hds-lee.de/

Your Job:

We are looking for a PhD student in machine learning to work within a project linked to the “Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE)”.

• Develop 3D+t image reconstruction methods in a cell microscopy setting using image sequences as well as focus stacks
• Investigate instance and panoptic segmentation for endosymbionts and track them over time
• Implement, train and test novel machine‑learning‑based solutions on top‑tier super‑computing hardware
• Work in an interdisciplinary team of engineers, computer scientists, and life scientists
• Regularly participate in international conferences to present your own work, and learn about state‑of‑the‑art machine learning and computer vision methods and their applications

Your Profile:

• Excellent Master’s degree in engineering, computer science or mathematics (or a related field), with a focus on computer vision, image processing, or machine learning
• Solid mathematical and physics background, distinct analytical skills
• Very good programming (Python, C++) and computer (Linux, Windows) skills
• Excellent cooperation and communication skills
• You enjoy to work within a diverse team in an international and interdisciplinary environment
• Very good English, both spoken and written. German language skills are not necessary but a plus
• High motivation and work ethics
• No prior biological experience is required, but curiosity about biological questions, collaborating closely with experimentalists, and working with real‑world data
• You share our passion for teaching computers how to see, preferably have done some previous research in this field (e.g., internships, research papers, etc.), and want to make an impact in a societally relevant application

In your application, please include a statement of research interest, CV, copies of exams, degrees and grades (transcript of records), a copy of your Master thesis (or a draft thereof), published articles or other relevant material such as letter(s) of recommendation (if applicable).

Our Offer:

We work on the very latest issues that impact our society and are offering you the chance to actively help in shaping the change! This HDS-LEE PhD position will be located at Forschungszentrum Jülich with strong links to RWTH Aachen. We offer ideal conditions for you to complete your doctoral degree:

• Outstanding scientific and technical infrastructures
• Working in an international and interdisciplinary environment at one of Europe’s largest research institutes
• Continuous scientific mentoring by your scientific advisors and opportunity to mentor students
• Unique HDS-LEE graduate school program (including data science courses, soft skill courses and annual retreats): https://www.hds-lee.de/about/
• A qualification that is highly valued in industry
• 30 days of annual leave and flexible working arrangements, including partial remote work
• Further development of your personal strengths, e.g. via a comprehensive training program; a structured program of continuing education and networking opportunities specifically for doctoral researchers via JuDocS, the Jülich Center for Doctoral Researchers and Supervisors: https://www.fz-juelich.de/judocs
• Targeted services for international employees, e.g. through our International Advisory Service

The position is limited to three years, with a possible one‑year extension. Pay is in line with 75% of pay group 13 of the Collective Agreement for the Public Service (TVöD‑Bund) and additionally 60 % of a monthly salary as special payment (“Christmas bonus”). The monthly salaries in euro can be found on the BMI website: https://go.fzj.de/bmi.tvoed.entgelt

Further information on doctoral degrees at Forschungszentrum Jülich (including its various branch offices) is available at https://www.fz-juelich.de/en/careers/phd

We welcome applications from people with diverse backgrounds, e.g. in terms of age, gender, disability, sexual orientation / identity, and social, ethnic and religious origin. A diverse and inclusive working environment with equal opportunities in which everyone can realize their potential is important to us.

The following links provide further information on diversity and equal opportunities: https://go.fzj.de/equality and on specific support options for women: https://go.fzj.de/womens-job-journey

About Jülich and the surrounding area: Forschungszentrum Jülich is one of the largest research centers in Europe, with excellent scientific equipment including one of the fastest supercomputers in the world. We are 7600 people located on a green campus offering an international and interdisciplinary working environment. Jülich is close to the border between Belgium, the Netherlands and Germany, and near the cultural centers Aachen, Bonn, Cologne, and Düsseldorf. The quality of life is exceptionally high and the atmosphere is both tolerant and inclusive. For an overview, please see ‘Facts, Figures, People’ ( https://www.fz-juelich.de/en/about-us/people/board-of-directors-and-organization/facts-figures ).