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

[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

Siebner, Thomas Hartwig, Stefan Fuglsang, Christopher Fugl Madelung, Annemette Løkkegaard, Flemming Bendtsen, Jens Dahlgaard Hove, Morten Damgaard, Jan Lysgård Madsen, and Hartwig Roman Siebner. “Gastric Emptying Is Not Delayed and Does Not Correlate With Attenuated Postprandial Blood Flow Increase in Medicated Patients With Early Parkinson’s Disease.” Frontiers in Neurology 13 (2022). https://www.frontiersin.org/article/10.3389/fneur.2022.828069.

Madelung, Christopher F., David Meder, Søren A. Fuglsang, Marta M. Marques, Vincent O. Boer, Kristoffer H. Madsen, Esben T. Petersen, Anne-Mette Hejl, Annemette Løkkegaard, and Hartwig R. Siebner. “Locus Coeruleus Shows a Spatial Pattern of Structural Disintegration in Parkinson’s Disease.” Movement Disorders 37, no. 3 (2022): 479–89. https://doi.org/10.1002/mds.28945.

Siebner, Thomas Hartwig, Christopher Fugl Madelung, Flemming Bendtsen, Annemette Løkkegaard, Jens Dahlgaard Hove, and Hartwig Roman Siebner. “Postprandial Increase in Mesenteric Blood Flow Is Attenuated in Parkinson’s Disease: A Dynamic PC-MRI Study.” Journal of Parkinson’s Disease 11, no. 2 (January 1, 2021): 545–57. https://doi.org/10.3233/JPD-202341.

Herz, Damian M., David Meder, Julia A. Camilleri, Simon B. Eickhoff, and Hartwig R. Siebner. “Brain Motor Network Changes in Parkinson’s Disease: Evidence from Meta-Analytic Modeling.” Movement Disorders 36, no. 5 (2021): 1180–90. https://doi.org/10.1002/mds.28468.

Lohse, Allan, David Meder, Silas Nielsen, Anders Elkjær Lund, Damian M Herz, Annemette Løkkegaard, and Hartwig R Siebner. “Low-Frequency Transcranial Stimulation of Pre-Supplementary Motor Area Alleviates Levodopa-Induced Dyskinesia in Parkinson’s Disease: A Randomized Cross-over Trial.” Brain Communications 2, no. 2 (July 1, 2020): fcaa147. https://doi.org/10.1093/braincomms/fcaa147.

Haagensen, Brian N., Damian M. Herz, David Meder, Kristoffer H. Madsen, Annemette Løkkegaard, and Hartwig R. Siebner. “Linking Brain Activity during Sequential Gambling to Impulse Control in Parkinson’s Disease.” NeuroImage: Clinical 27 (January 1, 2020): 102330. https://doi.org/10.1016/j.nicl.2020.102330.

Betts, Matthew J., Evgeniya Kirilina, Maria C. G. Otaduy, Dimo Ivanov, Julio Acosta-Cabronero, Martina F. Callaghan, Christian Lambert, et al. “Locus Coeruleus Imaging as a Biomarker for Noradrenergic Dysfunction in Neurodegenerative Diseases.” Brain 142, no. 9 (September 1, 2019): 2558–71. https://doi.org/10.1093/brain/awz193.

Meder, David, Damian Marc Herz, James Benedict Rowe, Stéphane Lehéricy, and Hartwig Roman Siebner. “The Role of Dopamine in the Brain - Lessons Learned from Parkinson’s Disease.” NeuroImage, Mapping diseased brains, 190 (April 15, 2019): 79–93. https://doi.org/10.1016/j.neuroimage.2018.11.021.

Irmen, Friederike, Andreas Horn, David Meder, Wolf-Julian Neumann, Philip Plettig, Gerd-Helge Schneider, Hartwig Roman Siebner, and Andrea A. Kühn. “Sensorimotor Subthalamic Stimulation Restores Risk-Reward Trade-off in Parkinson’s Disease.” Movement Disorders 34, no. 3 (2019): 366–76. https://doi.org/10.1002/mds.27576.

Meder, David, and Hartwig Roman Siebner. “Spectral Signatures of Neurodegenerative Diseases: How to Decipher Them?” Brain 141, no. 8 (August 1, 2018): 2241–44. https://doi.org/10.1093/brain/awy195.

Lehericy, Stéphane, David E. Vaillancourt, Klaus Seppi, Oury Monchi, Irena Rektorova, Angelo Antonini, Martin J. McKeown, et al. “The Role of High-Field Magnetic Resonance Imaging in Parkinsonian Disorders: Pushing the Boundaries Forward.” Movement Disorders 32, no. 4 (April 1, 2017): 510–25. https://doi.org/10.1002/mds.26968.

Correia, M. M., Rittman, T., Barnes, C. L., Coyle-Gilchrist, I. T., Ghosh, B., Hughes, L. E. & Rowe, J. B.
Towards accurate and unbiased imaging-based differentiation of Parkinson's disease, progressive supranuclear palsy and corticobasal syndrome.
Brain communications. 2, 1, p. 1-18, fcaa051. 2020.

Kaalund, S. S., Passamonti, L., Allinson, K. S. J., Murley, A. G., Robbins, T. W., Spillantini, M. G. & Rowe, J. B.
Locus coeruleus pathology in progressive supranuclear palsy, and its relation to disease severity.
Acta neuropathologica communications. 8, 1, p. 1-11, 11. 2020.

van der Vegt, J. P. M., Hulme, O. J., Madsen, K. H., Buhmann, C., Bloem, B. R., Münchau, A., Helmich, R. C. & Siebner, H. R.
Dopamine agonist treatment increases sensitivity to gamble outcomes in the hippocampus in de novo Parkinson's disease.
NeuroImage. Clinical. 28, p. 1-8, 102362. 2020.

Dogonowski, A. M., Andersen, K. W., Sellebjerg, F., Schreiber, K., Madsen, K. H. & Siebner, H. R.
Functional neuroimaging of recovery from motor conversion disorder: A case report.
NeuroImage. 190, p. 269-274, 2019.

Dubbioso, R., Manganelli, F., Siebner, H. R. & Di Lazzaro, V.
Fast Intracortical Sensory-Motor Integration: A Window Into the Pathophysiology of Parkinson's Disease.
Frontiers in Human Neuroscience. 13, p. 1-14, 111. 2019.

van Eimeren, T., Antonini, A., Berg, D., Bohnen, N., Ceravolo, R., Drzezga, A., Höglinger, G. U., Higuchi, M., Lehericy, S., Lewis, S., Monchi, O., Nestor, P., Ondrus, M., Pavese, N., Peralta, M. C., Piccini, P., Pineda-Pardo, J. Á., Rektorová, I., Rodríguez-Oroz, M., Rominger, A., Seppi, K., Stoessl, A. J., Tessitore, A., Thobois, S., Kaasinen, V., Wenning, G., Siebner, H. R., Strafella, A. P. & Rowe, J. B.
Neuroimaging biomarkers for clinical trials in atypical parkinsonian disorders: Proposal for a Neuroimaging Biomarker Utility System.
Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring. 11, p. 301-309, 2019.

Siebner, Hartwig R., David Meder, and Damian M. Herz. “FMRI in Parkinson’s Disease.” In FMRI: Basics and Clinical Applications, edited by Stephan Ulmer and Olav Jansen, 417–31. Cham: Springer International Publishing, 2020. https://doi.org/10.1007/978-3-030-41874-8_26

Thomsen, B. L. C., Herz, D. M., Siebner, H. R. & Løkkegaard, A.
Dyskinesier ved Parkinsons sygdom: opdatering om nye billeddannende metoder og behandlingsmuligheder.
Ugeskrift for Laeger. 12, 2017, p. 2-6, 2017.

Lehéricy, S., Vaillancourt, D. E., Seppi, K., Monchi, O., Rektorova, I., Antonini, A., McKeown, M. J., Masellis, M., Berg, D., Rowe, J. B., Lewis, S. J. G., Williams-Gray, C. H., Tessitore, A., Siebner, H. R. & International Parkinson and Movement Disorder Society -Neuroimaging Study Group.
The role of high-field magnetic resonance imaging in parkinsonian disorders: Pushing the boundaries forward.
Movement disorders. 32, 4, p. 510-525, 2017.

Løkkegaard A, Herz DM, Haagensen BN, Lorentzen AK, Eickhoff SB, Siebner HR (2016) Altered sensorimotor activation patterns in idiopathic dystonia - an activation likelihood estimation meta-analysis of functional brain imaging studies. Hum Brain Mapp 37:547-557.

Herz DM, Haagensen BN, Nielsen SH, Madsen KH, Løkkegaard A, Siebner HR (2016) Resting-state connectivity predicts levodopa-induced dyskinesias in Parkinson’s disease. Mov Disord 31:521-529.

Herz DM, Haagensen BN, Christensen MS, Madsen KH, Rowe JB, Løkkegaard A, Siebner HR (2015) Abnormal dopaminergic modulation of striato-cortical networks underlies levodopa-induced dyskinesias in humans. Brain 138:1658-1666.

Herz DM, Haagensen BN,Christensen MS, Madsen KH, Rowe J, Løkkegaard A, Siebner HR (2014) The acute brain response to levodopa heralds dyskinesias in Parkinson’s disease. Ann Neurol 75:829-836.

Herz DM, Eickhoff SB, Løkkegaard A, Siebner HR (2014) Functional neuroimaging of motor control in Parkinson’s disease: A meta-analysis. Hum Brain Mapp 35:3227-3237.

van der Vegt JPM, Hulme OJ, Zittel S, Madsen KH, Weiss MM, Buhmann C, Bloem BR, Münchau A, Siebner HR (2013) Attenuated neural response to gamble outcomes in drug-naive patients with Parkinson’s disease. Brain 136:1192-1203.