Jobs

PhD: Super-Resolution Visualisation and Control of Cellular Dynamics (1.0 FTE), 4 years

Description:

As a PhD student in the Smith lab you will develop a novel optical instrument for event-driven super-resolution visualization and high-precision control that enables real-time manipulation of key aspects of cell and developmental biology (smart microscopy). Ultimately, the goal is to establish microscopy-guided automated real-time control of biological processes. This will enable the automatic identification of certain cellular states or events (e.g. a cell in mitosis, a cell moving out of a niche) within a tissue followed by the automatic and iterative light-driven perturbations that can alter the cellular state or event (e.g. altering the orientation of the mitotic spindle, directing cells to specific locations). You will apply the framework that you develop here to our biological aims, for example, to perform super-resolution microscopy of cell division or other cellular reorganizations that occur in developing organoids or tumor initiation in organoids. In this exciting project, you will collaborate with different research groups within the IMAGINE! project. For the biological systems, you will work closely with the Kapitein, and Rios labs and for the optical hardware, information processing, and control algorithms with the Stallinga, Carroll, and Smal labs.

What are you going to do?

In this fully-funded 4-year project, you and your team members will:

• be embedded in a communicative interdisciplinary team that is formed by a collaboration between research groups at University of Utrecht, Princess Máxima Center for Pediatric Oncology, Erasmus Medical Centre and the TU Delft;
• build on our experience with optical design and instrumentation to design and build a novel microscope combining imaging and ontogenetic control;
• develop/apply simulations and data analysis routines to predict and verify instrument functionality;
• have the opportunity to obtain teaching experience and improve your leadership skills while guiding students;

Your profile:

We are looking for a highly motivated and creative candidate to join us in this unique project. We would like you to bring:

• A master’s degree or equivalent in Master of Science in Photonics, (bio)physics or similar;
• Experience in programming;
• Prior experience in artificial intelligence/machine learning is a plus, but not required;
• Intellectual curiosity for biology and the life sciences.

If you feel that this role is the perfect match, but you do not yet meet all the qualifications, we also welcome you to apply.

Doing a PhD at TU Delft requires English proficiency at a certain level to ensure that the candidate is able to communicate and interact well, participate in English-taught Doctoral Education courses, and write scientific articles and a final thesis. For more details please check the Graduate Schools Admission Requirements.

You can still apply for this position.

PhD: Software engineer for bio-image “on-the-fly” analysis and smart microscopy (1.0 FTE), 4 years

Description:

Until recently, processing and analysis of microscopy experiments has been limited to post hoc analysis. However, recent developments in microscopy systems now allow for interaction with microscopes during the process of imaging, allowing for “on-the-fly” analysis of data and event-driven adaptation of the imaging experiment based on this analysis. This opens the possibility for a whole new way of performing microscopy experiments.

One such possibility is in the analysis of cell behaviour and subsequent event-driven adaptations in real-time. We recently developed BEHAV3D (Dekkers et al. 2022), a technology platform that provides a way to segment and track cells over time and analyse their behavioural patterns. Currently, this analysis is performed post hoc, but for next-generation BEHAV3D you will develop “on-the-fly” deep-learning approaches capable of detecting and segmenting single cells and subsequent tracking to monitor cell dynamics and classify behavior in real-time.

In collaboration with the Kapitein lab these robust computational methods will form the foundation for developing smart microscopy systems. Ultimately, such systems will allow for real-time analysis of complex dynamic scenarios and selection of single cells with specific dynamics and perturbations to perform light-driven alterations of the cellular state in collaboration with other members of the Imagine consortium including the Smith lab.

Your profile:

• Master’s degree (or equivalent) in artificial intelligence, software engineering, physics, biology or similar
• background in some of these areas: computational science, software development, image analysis, artificial intelligence
• highly motivated and creative
• skill set: problem solving, analytical thinking, fluent in written and spoken English
• interest to work in a highly collaborative and interdisciplinary environment

For more information on the job offer and to apply follow this link.

You can still apply for this position.

PhD: Real-Time Image Analysis for Smart Microscopy (1.0 FTE), 4 years

Description:

In this PhD position at Erasmus MC – University Medical Center Rotterdam, you will develop methods and algorithms for image processing and data analysis based on Bayesian statistics and modern AI approaches to enable fully automated functioning of a smart microscopy system.

You will work together with the groups within the IMAGINE! Project. In collaboration with the groups of Prof. Kapitein, Prof. Stallinga and Dr. Smith, the goal is to establish methods for real-time analysis of (sub)cellular dynamics to facilitate on-the-fly optimisation of acquisition parameters as well as automated control over biological processes. The developed image processing techniques will enable real-time tracking of cells and intracellular objects, and classification of motion patterns in terms of healthy, diseased or suspicious behaviour or function.

Your profile:

We are looking for a highly motivated and creative candidate to join us in this unique project. We would like you to bring:

• a Master’s degree (or equivalent) in Computer Science, Applied Mathematics, Statistics, Nanobiology, Biophysics or a related field;
• a background in computer vision, statistics and machine learning, programming in Python, Java and C/C++;
• analytical and problem solving skills;
• proficiency in written and spoken English.

You can still apply for this position.

Postdoc: Optogenetic control of cell division and cell fate in C. elegans (1.0 FTE), 3 years

Description:

You will develop methods for laser-light mediated control of the orientation of cell division in the animal model C. elegans. In follow up studies, you will determine how the division orientation affects the fate and division pattern of daughter cells, based in part on super-resolution microscopy.

You will work together with the groups within the IMAGINE! project who also work on these systems and contribute to similar analyses in vivo (in particular the Kapitein Lab of Utrecht University). The overall goal is to acquire automated real-time (optogenetic) control strategies to steer processes within native cells in their tissue environment, as an important strategy for dissecting the molecular mechanisms and underlying principles of animal development.

Your profile:

We are looking for a highly motivated and creative candidate to join us in this unique project. We would like you to bring:

• A PhD degree (or equivalent) in Biology, Biomedical Sciences or a related field;
• high affinity for molecular biology;
• previous experience with independent research, and preferably with genetic model organisms and advanced microscopy;
• training in scientific writing, communication and presentation in English;
• motivation to work on a challenging project in a multidisciplinary and international research team.

You can still apply for this position.