PhD doctoral candidate position (m/f/d)

Überblick

This is a 3-year PhD position, in the frame of a Horizon Europe MSCA-Doctoral Network (DN) program (Funded by EU, GA: 101168976) entitled “Autonomous Scanning Probe Microscopy for Life Sciences and Medicine powered by Artificial Intelligence (SPM4.0)” that involves 10 research centers/academic institutions and 3 companies.

The SPM4.0 Consortium / Background

Artificial Intelligence (AI) is pushing forward the Industrial Revolution 4.0, which is transforming many areas of Society, including Science and Technology. Nanoscopy, a recognized pillar of the research and manufacture of Nanotechnology-based products, is among the areas that more quickly is adopting AI. Machine learning algorithms are being developed and integrated in microscopes for its autonomous operation and in software toolboxes for the automatic analysis of large volumes of microscopy data. Scanning Probe Microscopy is particularly active in this integration with a special focus in the Life Sciences and Medical fields. Scanning probe microscopes (SPMs) powered by machine learning are expected to enable the autonomous and label-free nanoscale structural and functional (mechanical and electric) imaging of living cells and functional biomolecules in their native conditions, something never achieved in nanoscopic imaging. The objective of the SPM4.0 Doctoral Network is to train a new generation of researchers in the science and technology of autonomous Scanning Probe Microscopes powered by Artificial Intelligence for applications in the Life Science and Medical fields. The researchers of the network will acquire a state-of-the-art multidisciplinary scientific training in advanced scanning probe microscopy and machine learning and in their biological and medical applications. In addition, they will receive training on complementary and transferable skills to increase their employability perspectives and to qualify them to access to responsibility job positions in the private and public sectors. The final aim is to promote the wide adoption of SPM4.0 technologies in public and private research centers and in industrial and metrology institutions and to explore new horizons in the Life Sciences and Medical sectors regarding label-free nanoscopic cell imaging, illness diagnosis, or drug nanocarrier development, consolidating Europe as world leader.The Bruker JPK BioAFM Business is the global market leader for atomic force microscopes (AFM) and optical tweezers (OT), scientific instruments used for biomolecular and cellular imaging, as well as force measurements on single molecules, cells and tissues. These high-performance instruments are developed, produced, and supported at the Bruker facility in Berlin, Germany, and sold worldwide.

For our Berlin Development Team, we are looking for a PhD Doctoral Candidate (m/f/d)

The project work will be performed in collaboration with the Charité University Hospital Berlin (Charité Universitätsmedizin Berlin), Germany, in the Elastography Group of the Department of Radiology and under the supervision of Prof. Ingolf Sack. The candidate will be enrolled in the doctoral degree programme at Charité and will profit additionally from the rich scientific landscape of the Berlin metropolitan region.

Objectives of the PhD

• To develop AI/ML solutions to identify cells and regions of interest (ROIs) in optical microscopy or topographic AFM images and define scanning areas automatically.
• To develop AI/ML solutions to autonomously set optimal scanning parameters for AFM topographic imaging and elastic property measurements of living cells and tissue samples.
• To integrate the developed neural networks and robotic control into an autonomous AFM system for topographic, nanomechanical, and nanoelectrical imaging of living cells and tissue. To validate the operation of the system by non-expert users.

Planned secondments

• University of Gothenburg, secondments of 4 and 2 months to develop machine learning methods for autonomous microscopy, to be supervised by Prof. G. Volpe.
• Instituto de Ciencia de Materiales de Madrid (CSIC), 2 months to implement quantitative functional SPM of living cells, supervised by Prof. R. Garcia.

Aufgaben/Verantwortlichkeiten

• Implement and assess AI/ML solutions for AFM automation (detection of ROIs, setting of optimal scanning parameters, …)
• Design and perform appropriate experiments to gather data for AI/ML training on live cells, tissues and model soft materials
• Develop concepts, logic and handling (user-story) to guide the decisions necessary for software development projects
• Contribute to a team developing scientific software for instrument control in diverse areas including GUI, data analysis and instrument control
• Close collaboration between the Bruker BioAFM development team and the Charité Elastography Group of Prof. Ingolf Sack
• Contribute to SPM4.0 Marie Curie Project communications, meetings and reports

Qualifikationen

Required project specific qualifications and skills

• Degree and Master on any field in Physics, Mathematics, Biotechnology or Engineering (completed before contact starting date), no Doctoral degree yet
• Experience in laboratory-based measurements and instrument control (AFM / SPM or related technique beneficial)
• Strong skills in Python (scripting, script-based data analysis and object-oriented development all beneficial)
• Basic knowledge about AI/ML and experience with their corresponding Python toolkits
• Strong communication skills and a team-oriented working style
• Proficiency in English
• Ability to maintain accurate and up to date records
• Ability to organise and prioritise own work and organise research within the project schedule
• Computer literacy, analytical skills and effective team working

Marie-Curie fellowship mobility requirement

At the time of recruitment for this project, candidates must not have resided or carried out their main activity (work or studies) in Germany for more than 12 months in the 3 years immediately prior to their recruitment.

Benefits

• 3-year full-time employment contract
• Gross salary of 3300 € - 3700 € approximately, depending on the family status at the time of the recruitment, according to the MSCA-DN regulations
• Working in a multidisciplinary environment at the interface between academic and commercial development
• Secondments at other institutions within the SPM4.0 Consortium
• Enrolment in the Doctoral degree programme of the Research training group BIOQIC at Charité University Hospital Berlin