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BIOLab PhD Position 4/4 Deep learning and smart super-resolution microscopy

Technische Universiteit Delft

City:

Delft, South Holland

Country:

Netherlands

Job Description

The position is based in the Grußmayer lab at the Department of Bionanoscience (AS faculty) under joint supervision of Kristin Grußmayer and Nergis Tömen from the Computer Vision Lab in the Department of Intelligent Systems (EEMCS faculty). The Grußmayer lab develops advanced 3D light microscopy methods to perform quantitative studies in live cells to answer fundamental questions in molecular and cell biology e.g., to understand neurodegenerative diseases. We combine label-free and super-resolution fluorescence microscopy, a set of techniques that circumvent the optical diffraction limit by clever experimental strategies and sophisticated image reconstruction. Yet, the used light doses often harm cells and imaging at molecular resolution is slow which poses significant challenges for live cell studies.

You will focus on incorporating feedback in decision-making routines and develop new technology for super-resolution microscopy. In the process, you will use inductive priors and domain-specific knowledge to improve and develop algorithms for bio-imaging using state-of-the-art deep neuronal networks (CNNs and transformer models) and classical image analysis tools in order to predict, interpolate and extrapolate biologically-relevant time series from imaging data in a data-efficient way. This will allow information-enriched longitudinal super-resolution imaging by minimizing photodamage through smart adaptive choice of microscopy modality with optimal imaging parameters (adaptation of imaging light dose, speed & resolution, AI enhanced vs true super-resolution, structural & functional imaging). You will closely interact with experimentalists in the Grußmayer Lab who work on optics and use microscopy to study biology and with other computer scientists in the Computer Vision Lab who study efficient machine learning. The PhD position is primarily focused on computational development, but depending on your interests, the work can include microscopy experiments.

This one of four PhD postions within the BIOLAB, for a complete overview check: https://www.tudelft.nl/ai/biolab

In the Biomedical Intervention Optimization lab (BIOlab), experts in computer vision (Tömen), reinforcement learning (Böhmer), neural architecture (Brinks), deep learning and computational physics (Perkó), and biomedical imaging (Gruβmayer, Carroll) join forces to create high-efficiency, real-time, AI-driven feedback and control in biomedical applications.

Requirements

To qualify for this position you must have:

An MSc degree (or equivalent) in applied physics, biomedical engineering, computer science or a strongly related field.

Demonstrated experience in programming in at least one current language (e.g., Python, Matlab, C/C++).

A proven record and interest in further developing modelling, programming and analytical and scientific writing skills.

Strong affinity and enthusiasm for state-of-the-art deep learning methods and their application in microscopy.

Wide-ranging interdisciplinary interests, affinity for biophysical methods and data analysis and intellectual curiosity for biology and the life sciences.

Demonstrated ability to be results oriented, applying creativity and out-of-the-box thinking to produce innovative concepts and solutions.

Demonstrated proficiency in expressing yourself verbally and in writing in English, proven affinity for scientific writing.

The ability to work in a team and take initiative.

Affinity for teaching and guiding students.

To be a strong candidate for this position, it is nice - but not necessary - if you have:

Background in optics and/or super-resolution microscopy and/or image processing.

Prior experience in artificial intelligence/machine learning/data science.

Demonstrated experience with convolutional neural networks and/or transformer architectures.

Proven familiarity with modern deep learning libraries (PyTorch, TensorFlow, PyMC3, KERAS-RL).

Conditions of employment

You will receive a 5-year contract and will be deployed for AI-related education for the usual teaching effort for PhD candidates in the faculty plus an additional 20%. The extra year compared to the usual 4-year contract accommodates the 20% additional AI, Data and Digitalisation education related activities. All team members have many opportunities for self-development. You will be a member of the thriving TU Delft AI Lab community that fosters cross-fertilization between talents with different expertise and disciplines.

TU Delft (Delft University of Technology)

Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society. For generations, our engineers have proven to be entrepreneurial problem-solvers, both in business and in a social context. At TU Delft we embrace diversity and aim to be as inclusive as possible (see our Code of Conduct). Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale.

Challenge. Change. Impact!

Biomedical Intervention Optimization lab (BIOlab)

This position is connected to the Biomedical Intervention Optimization lab (BIOlab). BIOLab is a new TU Delft Artificial Intelligence Lab. Artificial Intelligence, Data and Digitalisation are becoming increasingly important when looking for answers to major scientific and societal challenges. In a TU Delft AI Lab, experts in ‘the fundamentals of AI technology’ along with experts in ‘AI challenges’ run a shared lab.

As a PhD, you will work with at least two academic members of staff and three other PhD candidates. In total TU Delft will establish 24 TU Delft AI Labs, where 48 Tenure Trackers and 96 PhD candidates will have the opportunity to push the boundaries of science using AI. Each team is driven by research questions which arise from scientific and societal challenges, and contribute to the development and execution of domain specific education.

Goal of the Biomedical Intervention Optimization lab (BIOlab)

Modern machine learning algorithms have achieved unprecedented accuracy in image and video understanding tasks by purely learning from data. These powerful abilities come at the price of enormous amounts of training data, memory and computational requirements. However, those resources are rarely available to real-time feedback systems in medical intervention and biomedical research.

The lab will focus on improving the efficiency of machine learning algorithms by designing novel artificial neural network architectures, developing new reinforcement learning and generative algorithms, and incorporating biologically-inspired neural network models. These newly developed concepts and algorithms will be applied to a wide range of problems in biomedical applications, such as optimizing tumor irradiation protocols with missing information, and in smart (super-resolution) microscopy to limit irradiation damage to delicate living samples.

With more than 1,000 employees, including 135 pioneering principal investigators, as well as a population of about 3,400 passionate students, the Faculty of Applied Sciences is an inspiring scientific ecosystem. Focusing on key enabling technologies, such as quantum- and nanotechnology, photonics, biotechnology, synthetic biology and materials for energy storage and conversion, our faculty aims to provide solutions to important problems of the 21st century.

To that end, we train students in broad Bachelor's and specialist Master's programmes with a strong research component. Our scientists conduct ground-breaking fundamental and applied research in the fields of Life and Health Science & Technology, Nanoscience, Chemical Engineering, Radiation Science & Technology, and Engineering Physics. We are also training the next generation of high school teachers and science communicators.

Click here to go to the website of the Faculty of Applied Sciences.

Additional information

For information about this (super-resoltion AI) vacancy and the selection procedure, please contact Kristin grußmayer, Assistant Professor, email: K.S.Grussmayer@tudelft.nl. Please include “BIOLab_WP4” in the subject of your email

More information about the TU Delft AI Initiative can be found here.

Application procedure

Are you interested in this vacancy? Please apply no later than 4 April 2022 via the online application platform. We will not process applications sent by email and/or post. Incomplete applications and applications not conforming to the specified format requirements will automatically be disqualified and will not be evaluated.

Submit The Following Via The Online Application

Motivation letter (1 page, A4 size, font size 12, PDF format), highlighting past achievements that demonstrate your relevant competence and specific interest and enthusiasm for this project.

Your CV (PDF format), including contact details of two references who we can contact if needed to attest to your academic attitude, skills and work ethic.

A summary of your M.Sc. thesis (1 page, A4, size 12, PDF format).

A list of courses and grades taken for your B. Sc. and M. Sc. (or similar education).

If applicable, a paper that you have written in which you demonstrate your writing skills (PDF format).

A pre-employment screening can be part of the selection procedure.

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