Postdoctoral Researcher in bioimage informatics and machine learning

Updated: about 1 month ago
Deadline: 31 May 2024

NORPOD is a collaborative postdoctoral program of the Nordic EMBL Partnership for Molecular Medicine . The partnership is a network of four national research centers across the Nordics and the European Molecular Biology Laboratory (EMBL) , with complementary research expertise at the forefront of molecular medicine research. With the NORPOD program, the Nordic EMBL Partnership aims to foster the next generation of researchers in molecular medicine by implementing joint postdoctoral research projects to nurture strong competences and research excellence.

FIMM is currently seeking a Postdoctoral Researcher to join the Bioimage Profiling group, in collaboration with the Dr. Chao Sun’s Lab at DANDRITE, through the NORPOD program.

Summary of the project
Pyramidal neurons in the mammalian cortex use complex dendrites to integrate input from diverse brain regions in a parallel manner. To enable parallel processing, local intracellular organelles involved in synaptic metabolism such as the endoplasmic reticulum (ER) and mitochondria are fine-tuned to local synaptic function. So far, we do not have a complete landscape of ER and mitochondria distribution in individual neurons. This project will 1) mine existing electron microscopy (EM) connectomics databases to reconstruct the ER and mitochondria landscape for individual cortical pyramidal neurons and investigate this organelle landscape in relation to known electrophysiological features of individual neurons.

The postdoctoral researcher will analyze large 3D electron microscopy volumes to study the organelle landscape in individual pyramidal neurons of the mouse cortex. This includes deep learning-based segmentation of organelles to reconstruct the spatial landscape of these organelles. Further, the postdoctoral researcher will study spatial correlation of these organelles in dendritic branches of cortical layers and reconstruct the landscape of inter-organelle contacts in neurons.

Skills, expertise and/or qualifications
We expect a successful candidate to have a PhD degree from a relevant field with skills and experience in image analysis and machine learning. Familiarity with the volumetric microscopy image data and statistical methods are an asset, as well as a strong publication record in a relevant field. Good written and oral communication skills in English are expected. Proven international mobility is highly desirable. Experiences in collaborative research and project management is a must.

Research group descriptions
The Bioimage Profiling group led by Dr. Lassi Paavolainen at FIMM focuses on uncovering complex information from bioimages using machine learning. The group develops novel deep learning solutions for bioimage analysis, studies various machine learning approaches to create generalizable models, and applies these methods and models to profile cell and tissue samples imaged using 2/3D microscopy. The group is specifically focused on applying self-supervised representation learning and generative AI in computer vision to improve knowledge of disease and function of cells and tissues with the goal of using this information to treat human diseases.

The Synaptic Logistics Lab led by Dr. Chao Sun at DANDRITE ( investigates the molecular homeostasis brain synapses using quantitative in situ single-molecule approaches such as super-resolution microscopy as well as subcellular biochemistry and proteomics.


The NORPOD Fellow will be employed at the Bioimage Profiling group (FIMM, University of Helsinki, Finland). To promote collaboration between the two groups, this position will involve regular visits to and communication with the Synaptic Logistics Lab (DANDRITE, University of Aarhus, Denmark). Successful candidates are expected to travel between the labs to conduct work required for the research project, foster synergies and advance our goals. Expenses related to the research visits will be covered.

Contract & salary
The job is for a fixed term of 2.5 years. A trial period of 6 months will be applied. Salary will depend upon the applicant's level of skills, knowledge, and abilities and is based on the university salary system. The starting salary will be ca. 3,600 – 3,800 euros/month, depending on the appointee’s qualifications and experience and including a salary component based on personal performance. Standard Finnish pension benefits and occupational health care are provided for University employees. We welcome applicants from a variety of gender identities, linguistic and cultural backgrounds.
Selection process

●    The collaborating PIs of the research project will shortlist and video interview the top candidates.

●    Top candidates will be invited for an online interview, conducted by an independent selection panel where they will also be given the opportunity to pitch the project plan.

●    NORPOD Fellowships will be awarded based on the recommendation of the selection panel.

How to apply: 
The application should include (i) CV with a complete list of scientific publications, (II) a one-page statement of motivation for applying for this position, (iii) contact information of at least two reference persons who have agreed to provide a written statement on behalf of the applicant.
To apply, please submit the application through the University of Helsinki electronic recruitment system by clicking on Apply for job. Internal applicants (i.e., current employees of the University of Helsinki) please submit your applications through SAP Fiori
Please apply no later than 31st of May 2024

The University of Helsinki is an international scientific community of 40,000 students and researchers. It is one of the leading multidisciplinary research universities and ranks among the top 100 international universities in the world.
The Institute for Molecular Medicine Finland (FIMM) is an international research unit focusing on human genomics and personalised medicine at the Helsinki Institute of Life Science (HiLIFE) of the University of Helsinki - a leading Nordic university with a strong commitment to life science research. As part of Academic Medical Center Helsinki in Meilahti campus FIMM collaborates locally with the Faculty of Medicine, Helsinki University Hospital and National Institute for Health and Welfare. FIMM is part of the Nordic EMBL Partnership for Molecular Medicine, composed of the European Molecular Biology Laboratory (EMBL) and the centres for molecular medicine in Norway, Sweden and Denmark, and the EU-LIFE Community.

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