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[EXPIRED] The Capital Region of Copenhagen is looking for a PhD candidate in Machine Learning for Neuronal Feature Identification in 3D Microscopic Imaging - DTU Compute

Do you want to join a multidisciplinary team working with a new 3D optical imaging technology and develop machine learning models to map in the brain neuronal and cellular objects, their geometry, density and organization? Are you interested in learning about 3D imaging analysis, brain anatomy, collect your own high-quality microscopic data as well as generating synthetic cellular environments to evaluate and train your model? Are you intrigued by solving challenges working with big data? Are you eager to develop innovative solutions in a groundbreaking project at the intersection of neuroimaging and machine learning? If yes, we encourage you to apply and join our team!

DTU Compute’s Section for Visual Computing is opening a PhD position in Machine Learning for Neuronal Feature Identification in 3D Microscopic Imaging. The project is financed by the Independent Research Fund Denmark – and aims at modelling neuronal anatomical compartments from 3D Light-Sheet (label-free- and fluorescence- based) microscopic imaging data. The project will also be carried out at the Danish Research Centre for MR at Copenhagen University Hospital Hvidovre, and in collaboration with IRB Barcelona: Institute for Research in Biomedicine (Barcelona, Spain).

Qualifications

  • Master's degree in visual computing, computational science and engineering, or equivalent, with focus on machine learning,
  • Experience in Python programming is highly desired,
  • Practical experience working with Machine Learning within the image processing and analysis field will be a plus,
  • Experience in experimental bioimaging will be highly valued: Interest in data collection, understanding of image data quality concepts for ensuring optimal modelling purposes. 
  • Interest in learning light-sheet based physics underpinning microscopic image contrast to be modelled, 
  • You have a good team spirit, innovative and constructive thinking, research excitement. Good English communication skills are essential.

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

Approval and Enrolment 
The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see DTU's rules for the PhD education.

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

You can read more about the Microstructure and Plasticity group you be part of, the Visual Computing section and the Department of Applied Mathematics and Computer Science at DTU as well as the Danish Research Centre for MR.

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark. Furthermore, you have the option of joining our monthly free seminar “PhD relocation to Denmark and startup “Zoom” seminar” for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU. 


DTU Compute has a total staff of 400 including 100 faculty members and 130 Ph.D. students. We offer introductory courses in mathematics, statistics, and computer science to all engineering programmes at DTU and specialised courses to the mathematics, computer science, and other programmes. We offer continuing education courses and scientific advice within our research disciplines and provide a portfolio of innovation activities for students and employees.

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear mission to develop and create value using science and engineering to benefit society. That mission lives on today. DTU has 13,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.

 

Selected Publications

Dunås T, Wåhlin A, Nyberg L, Boraxbekk C-J. 2021. Multimodal Image Analysis of Apparent Brain Age Identifies Physical Fitness as Predictor of Brain Maintenance. Cerebral Cortex. 31(7):3393-3407. https://doi.org/10.1093/cercor/bhab019

Hansen AL, Boraxbekk C-J, Petersen ET, Paulson OB, Andersen O, Siebner HR, Marsman A. 2021. Do glia provide the link between low-grade systemic inflammation and normal cognitive ageing? A 1H magnetic resonance spectroscopy study at 7 tesla. Journal of Neurochemistry. 159(1):185-196.

Nyberg L, Magnussen F, Lundquist A, Baaré W, Bartrés-Faz D, Bertram L, Boraxbekk CJ, Brandmaier AM, Drevon CA, Ebmeier K, Ghisletta P, Henson RN, Junqué C, Kievit R, Kleemeyer M, Knights E, Kühn S, Lindenberger U, Penninx BWJH, Pudas S, Sørensen Ø, Vaqué-Alcázar L, Walhovd KB, Fjell AM. 2021. Educational attainment does not influence brain aging. Proceedings of the National Academy of Sciences of the United States of America. 118(18):1-3. https://doi.org/10.1073/pnas.2101644118

Sandberg P, Boraxbekk C-J, Zogaj I, Nyberg L. 2021. Ancient Mnemonic in New Format-Episodic Memory Training With the Method of Loci in a Smart Phone Application. Journals of Gerontology - Series B Psychological Sciences and Social Sciences. 76(4):681-691. https://doi.org/10.1093/geronb/gbaa216

Vidal-Pineiro D, Wang Y, Krogsrud SK, Amlien IK, Baaré WF, Bartres-Faz D, Bertram L, Brandmaier AM, Drevon CA, Düzel S, Ebmeier K, Henson RN, Junqué C, Kievit RA, Kühn S, Leonardsen E, Lindenberger U, Madsen KS, Magnussen F, Mowinckel AM, Nyberg L, Roe JM, Segura B, Smith SM, Sørensen Ø, Suri S, Westerhausen R, Zalesky A, Zsoldos E, Walhovd KB, Fjell A. 2021. Individual variations in 'brain age' relate to early-life factors more than to longitudinal brain change. eLife. 10:1-19. https://doi.org/10.7554/eLife.69995

Lind, A., Boraxbekk, C.J., Petersen, E.T., Paulsson, O., Siebner, H., & Marsman, A. (2020). Regional myo-inositol, creatine and choline levels are higher at older age and scale negatively with visuo-spatial working memory: A cross-sectional proton MR spectroscopy study at 7 tesla on normal cognitive ageing. Journal of Neuroscience, 40(42), 8149-8159.

Nyberg, L., Boraxbekk, C.J., Eriksson Sörman, D., Hansson, P., Herlitz, A., Kauppi, K., Ljungberg, J.K., Lövheim, H., Lundquist, A., Nordin Adolfsson, A., Oudin, A., Pudas, S., Rönnlund, M., Stiernstedt, M., Sundström, A., & Adolfsson, R. (2020). Biological and environmental predictors of heterogeneity in neurocognitive ageing: Evidence from Betula and other longitudinal studies. Ageing Research Reviews.

Gylling AT, Bloch-Ibenfeldt M, Eriksen CS, Ziegler AK, Wimmelmann CL, Baekgaard M, Boraxbekk CJ, Siebner HR, Mortensen EL, & Kjaer M. (2020). Maintenance of muscle strength following a one-year resistance training program in older adults. Experimental Gerontology, 139.

Eskilsson, T., Fjellman-Wiklund, A., Ek Malmer, E., Stigsdotter Neely, A., Malmberg Gavelin, H., Slunga Järvholm, L., Boraxbekk, C-J. & Nordin, M.(2020). Hopeful struggling for health: Experiences of participating in computerized cognitive training and aerobic training for persons with stress-related exhaustion disorder. Scandinavian Journal of Psychology.

Friedman, B. B., Suri, S., Solé-Padullés, C., Düzel, S., Drevon, C. A., Baaré, W. F. C., Bartrés-Faz, D., Fjell, A. M., Johansen-Berg, H., Madsen, K. S., Nyberg, L., Penninx, B. W. J. H., Sexton, C., Walhovd, K. B., Zsoldos, E. & Budin-Ljøsne, I. (2020). Are People Ready for Personalized Brain Health? Perspectives of Research Participants in the Lifebrain Consortium. The Gerontologist.

Hansen, A. L., Boraxbekk, C-J., Petersen, E. T., Paulson, O. B., Siebner, H. R. & Marsman, A. (2020). Regional glia-related metabolite levels are higher at older age and scale negatively with visuo-spatial working memory: A cross-sectional proton MR spectroscopy study at 7 tesla on normal cognitive ageing. Cold Spring Harbor Protocols. 36 p., 864496.

Karalija, N., Jonassson, L., Johansson, J., Papenberg, G., Salami, A., Andersson, M., Riklund, K., Nyberg, L. & Boraxbekk, C-J. (2020). High long-term test-retest reliability for extrastriatal 11C-raclopride binding in healthy older adults.
Journal of cerebral blood flow and metabolism.

Wheeler, M. J., Green, D. J., Ellis, K. A., Cerin, E., Heinonen, I., Naylor, L. H., Larsen, R., Wennberg, P., Boraxbekk, C-J., Lewis, J., Eikelis, N., Lautenschlager, N. T., Kingwell, B. A., Lambert, G., Owen, N. & Dunstan, D. W. (2020).
Distinct effects of acute exercise and breaks in sitting on working memory and executive function in older adults: a three-arm, randomised cross-over trial to evaluate the effects of exercise with and without breaks in sitting on cognition.
British Journal of Sports Medicine.

Bangsbo, J., Blackwell, J., Boraxbekk, C-J., Caserotti, P., Dela, F., Evans, A. B., Jespersen, A. P., Gliemann, L., Kramer, A. F., Lundbye-Jensen, J., Mortensen, E. L., Lassen, A. J., Gow, A. J., Harridge, S. D. R., Hellsten, Y., Kjaer, M., Kujala, U. M., Rhodes, R. E., Pike, E. C. J., Skinner, T., Skovgaard, T., Troelsen, J., Tulle, E., Tully, M. A., van Uffelen, J. G. Z. & Viña, J. (2019). Copenhagen Consensus statement 2019: physical activity and ageing. British Journal of Sports Medicine. 53, 14, p. 856-858.

Bojsen-Møller, E., Boraxbekk, C-J., Ekblom, Ö., Blom, V. & Ekblom, M. M. (2019). Relationships between Physical Activity, Sedentary Behaviour and Cognitive Functions in Office Workers.
International Journal of Environmental Research and Public Health. 16, 23, p. 1-15, 4721.

Düzel, E., Acosta-Cabronero, J., Berron, D., Biessels, G. J., Björkman-Burtscher, I., Bottlaender, M., Bowtell, R., Buchem, M. V., Cardenas-Blanco, A., Boumezbeur, F., Chan, D., Clare, S., Costagli, M., de Rochefort, L., Fillmer, A., Gowland, P., Hansson, O., Hendrikse, J., Kraff, O., Ladd, M. E., Ronen, I., Petersen, E., Rowe, J. B., Siebner, H., Stoecker, T., Straub, S., Tosetti, M., Uludag, K., Vignaud, A., Zwanenburg, J. & Speck, O. (2019). European Ultrahigh-Field Imaging Network for Neurodegenerative Diseases (EUFIND). Alzheimer's & dementia (Amsterdam, Netherlands). 11, p. 538-549.

Hedlund, M., Lindelöf, N., Johansson, B., Boraxbekk, C-J. & Rosendahl, E. (2019). Development and Feasibility of a Regulated, Supramaximal High-Intensity Training Program Adapted for Older Individuals. Frontiers in physiology. 10, p. 1-12, 590.

Holm, S. K., Madsen, K. S., Vestergaard, M., Born, A. P., Paulson, O. B., Siebner, H. R., Uldall, P. & Baaré, W. F. C. (2019). Previous glucocorticoid treatment in childhood and adolescence is associated with long-term differences in subcortical grey matter volume and microstructure. NeuroImage. Clinical. 23, p. 1-11, 101825. 

Jonasson, L. S., Nyberg, L., Axelsson, J., Kramer, A. F., Riklund, K. & Boraxbekk, C-J. (2019). Higher striatal D2-receptor availability in aerobically fit older adults but non-selective intervention effects after aerobic versus resistance training. NeuroImage. 202, p. 1-10, 116044.

Magnusson, P. O., Boer, V. O., Marsman, A., Paulson, O. B., Hanson, L. G. & Petersen, E. T. (2019). Gamma-aminobutyric acid edited echo-planar spectroscopic imaging (EPSI) with MEGA-sLASER at 7T.
Magnetic Resonance in Medicine. 81, 2, p. 773-780.

Månsson, K. N. T., Lindqvist, D., Yang, L. L., Svanborg, C., Isung, J., Nilsonne, G., Bergman-Nordgren, L., El Alaoui, S., Hedman-Lagerlöf, E., Kraepelien, M., Högström, J., Andersson, G., Boraxbekk, C-J., Fischer, H., Lavebratt, C., Wolkowitz, O. M. & Furmark, T. (2019). Improvement in indices of cellular protection after psychological treatment for social anxiety disorder. Translational psychiatry. 9, p. 1-10, 340.

Marsman, A. & Pol, H. H. (2019). Glutamaterge neurotransmissie. Handboek schizofreniespectrumstoornissen. 2nd udg. De Tijdstroom/Boom, Bind 2019. p. 370-385..

Malmberg Gavelin, H., Eskilsson, T., Boraxbekk, C.J., Josefsson, M., Stigsdotter Neely, A., & Slunga Järvholm L. (2018). Rehabilitation for improved cognition in patients with stress-related exhaustion disorder: RECO – a randomized clinical trial. Stress.

Boraxbekk, C.-J. (2018). Non-invasive brain stimulation and neuro-enhancement in aging. Clinical Neurophysiology, 129, 464-65.

Baruël Johansen, L., Madsen, K. S., Andersen, K. W., Madsen, K. H., Siebner, H. R. & Baaré, W. F. C. (2017) Reduced orbitofrontal functional network centrality characterizes high neuroticism across childhood and adolescence.

Stomby, A., Otten, J., Ryberg, M., Nyberg, L., Olsson, T. & Boraxbekk, C-J. (2017). A Paleolithic Diet with and without Combined Aerobic and Resistance Exercise Increases Functional Brain Responses and Hippocampal Volume in Subjects with Type 2 Diabetes. Frontiers in Aging Neuroscience. 9, 391.

Jonasson, L. S., Axelsson, J., Riklund, K. & Boraxbekk, C.-J. (2017). Simulating effects of brain atrophy in longitudinal PET imaging with an anthropomorphic brain phantom.
Physics in Medicine and Biology. 62, 13, p. 5213-5227.

Gavelin, H. M., Neely, A. S., Andersson, M., Eskilsson, T., Järvholm, L. S. & Boraxbekk, C-J. (2017). Neural activation in stress-related exhaustion: Cross-sectional observations and interventional effects.
Psychiatry Research. 269, p. 17-25.

Flodin, P., Jonasson, L. S., Riklund, K., Nyberg, L. & Boraxbekk, C.-J. (2017). Does Aerobic Exercise Influence Intrinsic Brain Activity?: An Aerobic Exercise Intervention among Healthy Old Adults.Frontiers in Aging Neuroscience. 9, p. 267.

Eskilsson, T., Slunga Järvholm, L., Malmberg Gavelin, H., Stigsdotter Neely, A. & Boraxbekk, C-J. (2017). Aerobic training for improved memory in patients with stress-related exhaustion: a randomized controlled trial. BMC Psychiatry. 17, 322, p. 1-10, 322.

Bas-Hoogendam, J. M., van Steenbergen, H., Nienke Pannekoek, J., Fouche, J. P., Lochner, C., Hattingh, C. J., Cremers, H. R., Furmark, T., Månsson, K. N. T., Frick, A., Engman, J., Boraxbekk, C.-J., Carlbring, P., Andersson, G., Fredrikson, M., Straube, T., Peterburs, J., Klumpp, H., Phan, K. L., Roelofs, K., Veltman, D. J., van Tol, M. J., Stein, D. J. & van der Wee, N. J. A. (2017). Voxel-based morphometry multi-center mega-analysis of brain structure in social anxiety disorder. NeuroImage: Clinical. 16, p. 678-688.

Jonasson, L.S., Nyberg, L., Kramer, A.F., Lundquist, A., Riklund, K., & Boraxbekk, C.-J. (2017). Aerobic exercise intervention, cognitive performance, and brain structure: Results from the physical influences on brain in aging (PHIBRA) study. Frontiers in Aging Neuroscience; 8, 336.

Boraxbekk, C.-J., Salami, A., Wåhlin, A., & Nyberg, L. (2016). Physical activity over a decade modifies age-related decline in perfusion, gray matter volume, and functional connectivity of the posterior default mode network - a multimodal approach. NeuroImage; 131, 133-141

Group Members

Naiara Demnitz

Group Leader

Sussi Larsen

External Collaborators

Prof. Erik Lykke Mortensen

Department of Public Health, Copenhagen University

Prof. Michael Kjær

Department of Clinical Medicine, Bispebjerg Hospital, University of Copenhagen

Prof. Gunhild Waldemar

Department of Neurology, Copenhagen University Hospital Rigshospitalet 

Prof. Lars Nyberg

Umeå Center for  Functional Brain Imaging