Introduction to the vacant position: Researcher on SPM4.0 MSCA project

We offer a 3-years job in the framework of the Horizon Europe MSCA-Doctoral Network “Autonomous Scanning Probe Microscopy for Life Sciences and Medicine powered by Artificial Intelligence (SPM4.0)”. This project is funded by the European Union (GA: 101168976) and in total will involve 16 PhD positions distributed in 10 research centers/academic institutions and 3 companies from Spain, Sweden, France, Germany, Italy, Poland, Czech Republic and UK. The job at Czech Metrology Institute (CMI) has to be linked with a running PhD at the Central European Institute of Technology, Brno University of Technology (CEITEC BUT) who acts as an affiliated partner awarding an academic degree. In fulfillment of the MSCA rules, the PhD student has an obligation to work exclusively for the SPM4.0 doctoral network for the 36 months supported through the funds of the doctoral network (being offered in this job offer). The application to the PhD programme at CEITEC BUT has to be submitted first and admission to the PhD programme is needed for this job.

The SPM4.0 Project:

Aim of the SPM4.0 Project is to develop a novel generation of autonomous Scanning Probe Microscopes (SPM) powered by Artificial Intelligence (AI), transforming the way how SPMs are used in research and applications in the life sciences areas and namely in medicine. Machine learning algorithms have potential to enable fully autonomous operation of SPMs when measuring complex biological samples if software toolboxes for the automatic analysis of large volumes of microscopy data will be used. Scanning probe microscopes 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 SPM4.0 Doctoral Network will acquire 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 job positions in the private and public sectors. The final aim is to promote the wide adoption of autonomous, AI powered and life sciences focusing 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.

Czech Metrology Institute:

The Department of Nanometrology, Czech Metrology Institute, where this job would be run, has been working in the area of quantitative data processing in Scanning Probe Microscopy since 2003. Together with CEITEC BUT, CMI develops an open source software for SPM data processing Gwyddion (http://gwyddion.net) which will serve as a key platform for development of data processing tools within this job and related PhD study.

CEITEC, Brno University of Technology:

CEITEC, at which the related doctoral project will be run, is a leading scientific institution in the area of nanoscience and nanotechnology in Central Europe. CEITEC PhD school is an international and rapidly growing study programme allowing access to many state-of-the-art scientific facilities.

Brno is the second largest city in the Czech Republic. Almost 65 000 students are studying in Brno and 13 000 more are here due to mobility programmes (Erasmus+, Freemover etc.). There are five public, one state and four private higher education institutions, giving the city the distinction of having the highest per capita student population in the Czech Republic and creating a friendly and motivating atmosphere for students.

Job description and Doctoral Candidate Research Project:

The main objective of the research project is to develop fast data processing methods for processing force-distance-energy data coming from Scanning Probe Microscopy on surfaces relevant for life sciences research and medicine, including curve classification tools based on machine learning, providing both the curve quality feedback to the SPM controller and initial estimates for the nano-mechanical and electrical fits, with known measurement uncertainty related to data quality and data processing (col. CSIC, IBEC). This will be combined with research on potential speedup methods in fitting of large volumes of curves (e.g. using Field Programmable Gate Arrays, Graphics cards and machine learning), and finally will lead integration into the autonomous multiparametric SPM4.0s in cooperation with other partners. In parallel to this, aspects of machine learning explainability and uncertainty in SPM will be handled.

To achieve it the doctoral candidate will:

• Develop both machine learning based and conventional methods based data processing routines for force-distance and force-distance-energy data cubes.
• Contribute to Gwyddion open source software development to be used as a demonstrator platform for developed routines.
• Integrate the algorithms into autonomously running microscopes.
• Cooperate on the goals of SPM4.0 project by performing joint research with other doctoral candidates, visiting the partner institutions and attending training activities organized by the consortium.

Requirements for candidates:

Essential:

• Master (MSc) in Physics/Mathematics/Bioengineering/Data Science or related fields
• Self-critical, capacity to learn and bring knowledge, motivated and proactive
• Competencies and skills: Communication, Teamwork, Proactivity, Commitment, Collegiality, Integrity, Critical and Analytical thinking
• Programming and data analysis skills and willingness to develop them further.
• Excellent proficiency in English, both written and spoken.

Additional potential areas of experience considered in the selection procedure: 

• Machine learning
• Mechanical properties of biological tissues
• Scanning Probe Microscopy
• C/C++ programming experiences

Eligibility conditions according to the MSCA-DN rules:

• Candidates must NOT have a doctoral degree at the date of the starting of the contract.
• Candidates must be admitted to the related PhD. topic in the PhD. programme at CEITEC BUT (to be applied first) before starting the job, working on the thesis titled “Fast force volume SPM data interpretation for nano-mechanical and electrical analysis with known uncertainty”.
• Candidates must comply with the mobility rule: NOT have resided or carried out his/her main activity (living, work, studies, etc.) in the Host Institution Country (Czech Republic) for more than 12 months in the 36 months preceding the date of the starting of the contract (recruitment date).

We Offer:

• Number of available positions: 1
• Working conditions: 3-year full-time employment contract (Starting date 1st September 2025).
• A gross salary for the whole duration of the 3-year project of 96 818 € (in total). On top of it, there is a mobility allowance (up to 21 600 € in total) and family allowance (up to 17 820 € in total) according to MSCA-DN guidelines, depending on the family status of the candidate.
• Flexible schedule working hours, 25 working days of paid holidays.
• Secondments for a duration of 4 months at other institutions within the SPM4.0 Consortium.
• Opportunities to participate in national and international conferences and consortium meetings.
• Active participation on the very widely used software project Gwyddion together with the developer community.

How to apply:

Apply for the PhD project “Fast force volume SPM data interpretation for nano-mechanical and electrical analysis with known uncertainty” at BUT (https://www.euraxess.cz/jobs/321761). Send the PhD project application also to petr.klapetek@cmi.gov.cz to apply for the funding in parallel.

If you have any further question regarding your application, please contact us at petr.klapetek@cmi.gov.cz

Protection of personal data:

CMI guarantees that candidates' personal data are processed in accordance with the requirements of the EU General Data Protection Regulation (GDPR) and Law 3/2018 on Data Protection. Personal data will be processed solely for the purposes of the selection process.

Where to apply

Apply for the PhD project “Fast force volume SPM data interpretation for nano-mechanical and electrical analysis with known uncertainty” at BUT (https://www.euraxess.cz/jobs/321761). Send the PhD project application also to petr.klapetek@cmi.gov.cz to apply for the funding in parallel.

Requirements

Research Field

Physics » Other

Education Level

Master Degree or equivalent

Additional Information

Website for additional job details: http://nanometrologie.cz/en/msca.php

Work Location(s)

Number of offers available: 1

Company/Institute: Czech Metrology Institute

Country: Czech Republic