The group is affiliated with the University of Basel’s Department of Biomedical Engineering, the Neurology Department at University Hospital Basel, and the Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB).
ThINk Basel is composed of five principal investigators (Prof Cristina Granziera, Prof Dr Regina Schläger, PD Dr Katrin Parmar, PD Dr Athina Papadopoulos, and Prof Dr Oezguer Yaldizli) and their teams, amounting to 46 members.

Within this framework, Prof Cristina Granziera has the lead and coordination of the entire group as well as the direct supervision of a dynamic team of 26 professionals, including master’s and Ph.D. students, postdoctoral fellows, senior scientists, and research staff, all working collaboratively to advance neurology and neuroimaging research.

Our main research focus is the understanding of multiple sclerosis (MS) physiopathology, the identification of biomarkers of MS progression and therapy response, the development of new computational models of MS disease impact and evolution as well as the investigation of mechanisms of structural remodeling/regeneration within the central nervous system of patients with MS. To achieve these goals, we exploit the sensitivity and specificity of advanced quantitative magnetic resonance imaging and modern analysis methods including classical machine-learning techniques and deep-learning networks. The group is funded through a grant from the Swiss National Science Foundation (SNSF), the Hasler Foundation, the “Stiftung zur Förderung der gastroenterologischen und allgemeinen klinischen Forschung”, intramural funding of the University of Basel and corporate research grants. In 2024, we achieved some major milestones in the understanding of mechanisms underlying clinical worsening in people with MS as well as in the exploration of novel biomarkers for MS diagnosis and in the identification of novel methods to assess focal remyelination and novel features of MS pathology in postmortem studies. We have substantially contributed to advance the procedures for MS diagnosis by exploring the diagnostic value of cortical lesions and central vein sign in a large MAGNIMS study involving more than 1000 MS patients (Cagol A. et al., JAMA Neurol 2024).

Moreover, we have applied novel approaches based on the combination of multishell diffusion and magnetization transfer imaging that allowed us to identify lesion classes based on repair and damage features over time (Sanabria G, et al., Annals Neurol 2024) as well as based on myelin characteristics as derived by applying the chi separation method to quantitative-susceptibility mapping and multi-echo T2 data (Müller J. et al., Neurology 2024). In both studies, we have also obtained that the proportion of repaired lesions was related to the patients’ disability (Figure 4). In addition, we are pursuing the explorations postmortem both at 3T and 9.4 T in collaboration with the neuropathology team in Göttingen and with the medical physics team in Freiburg (Germany). In this context, we have developed ultra-high-resolution protocols at 9.4 T that have cellular resolution, as well as made novel observations related to the distribution and contribution to the diffusion signal of activated astrocytes (Callegari I. et al, ECTRIMS 2024 and Gkotsoulias D. et al., ECTRIMS and ISMSRM 2024).

PD Dr Athina Papadopoulou leads a team of seven doctoral and post-doctoral researchers, which focuses on the investigation of the retina and visual pathway in MS and other neuroinflammatory disorders as well as on the study of headache and central pain.

Applying OCT, quantitative MRI and evoked potentials in collaboration with the lab of electrophysiology and the team of Prof C. Granziera, the team investigates structural-functional associations along the visual pathway in people with MS (pwMS).

We showed that structural damage at the synapse-level of the thalamic Lateral geniculate node (LGN) may contribute to functional visual damage (Papadopoulou A. et al, Clinical Neurophysiology, 2024).

Furthermore, the group investigated in 2024 the role of retina markers to predict progression independent of relapses, so called “PIRA” (progression independent of relapse activity), in pwMS.

In the “REMIND” study (Retinal Markers In Neurological Diseases), which is funded by a SNF-“Ambizione” grant to Athina Papadopoulou, neuronal loss in the retina was related to increased rates of progression independent of relapses - (PIRA) (Burguet F. et al, ECTRIMS 2024). Moreover, In collaboration with the Department of Sport, Exercise and Health (Prof H. Hanssen), the team analyses retinal vessel diameter as measure of the impact of vascular comorbidities and as a marker of disability and treatment effects. The team also explores associations between OCT-derived retinal measures and imaging and body fluid biomarkers. In this context, we found a close relationship between neuronal retinal loss and serum Glial Fibrillary Acidic Protein levels (sGFAP) (Sellathurai et al., ECTIRMS 2024), while analysis using advanced MRI is ongoing.

Prof Regina Schlaeger leads a research team of 7 post-doctoral fellows, doctoral students and master students, which focuses on the investigation of motor neuron diseases and other genetic, neurodegenerative and inflammatory diseases of the spinal cord and cerebellum. The team is funded by several grants from private foundations as well as corporate research grants.

Currently several prospective imaging studies are ongoing that evaluate novel sequences and MR approaches developed by our partners in MR physics (Prof Olivier Bieri, Magnetic Resonance Physics & Methodology and PD Dr Santini, Basel Muscle MRI).

To validate these novel MR-sequences the team also conducts post-mortem studies in collaboration with the research groups of Prof Eva Scheuer and PD Dr Claudia Lenz, University of Basel as well as with the team of C. Granziera.

In 2024, Prof Regina Schlaeger’s team described the lateral corticospinal tract sign – a novel MRI marker for amyotrophic lateral sclerosis that distinguishes ALS from other forms of motor neuron diseases (Wendebourg et al., Radiology 2024). Based on rAMIRA imaging, a sequence developed by Matthias Weigel and Prof Oliver Bieri at the department of Radiological Physics, the group also investigated spinal cord gray and white matter atrophy and its association to clinical disability in ALS (Wendebourg et al., European Journal of Neurology, 2024) and spinal muscular atrophy (Kesenheimer et al., Journal of Neurology 2025).

Last, in collaboration with PD Dr Santini’s group and funded by the Swiss National Science Foundation (219674) the group also started working on novel multiparametric MRI methods for Myotonic Dystrophy Assessment and Management.

Prof Özgür Yaldizli leads a team of three research associates and two master students. In addition to their contribution to Multiscript (see WS 4) the group is investigating the role of the choroid plexus and is part of an international collaboration supported by an ERA-NET NEURON grant to study the significance of the choroid plexus in multiple sclerosis and chronic pain.

Finally PD Dr Katrin Parmar is an associate member of ThINk Basel. She currently works as senior consultant neurologist in Reha Rheinfelden. In this context, she plans studies using digital and imaging biomarkers for rehabilitation purposes.