Human Microstructural Connectomics: Computational Modelling and Validation with Histology and CLARITY

The Max Planck Institute for Human Cognitive and Brain Sciences (MPI CBS, Leipzig, Germany) has an opening for a PhD Position.

The position is available for three years and is part of a collaboration between MPI CBS (Alfred Anwander, Stefan Geyer), Department of Systems Neuroscience, Medical Center Hamburg-Eppendorf (Siawoosh Mohammadi), and Paul Flechsig Institute of Brain Research, University of Leipzig (Markus Morawski), entitled Human Microstructural Connectomics: Computational Modelling and Validation with Histology and CLARITY and funded by the DFG Priority Programme "Computational Connectomics". You will be embedded in a world-leading research environment with cutting-edge MRI hardware (the unique combination of a CONNECTOM and 7T MRI system in Continental Europe) and state-of-the-art histology (CLARITY-based clearing of human post-mortem tissue and analysis with light-sheet microscopy).
Project Description
The arrangement, length, and microstructural properties of long-range connections in the central nervous system (CNS) are of utmost importance for its functional organization because they determine how information is distributed across the brain. To date, diffusion magnetic resonance imaging (dMRI)-based tractography is the only in vivo technique for mapping structural long-range connections in the human brain. However, mapping from diffusion to fiber pathways is still ill-posed and has several major limitations. As a result, tractography algorithms can take "wrong turns" and produce false positive and false negative connections.

To address this problem, microstructure-informed tractography has been suggested. It is an emerging computational framework that associates each computed fiber tract with microstructural properties, e.g., metrics for axon diameter or density, using the dMRI technique.

In this highly inter-disciplinary project, we will develop a computational framework for microstructure-informed tractography using multi-modal quantitative MRI at an unprecedented ultra-high spatial resolution (660 µm). You will be involved in developing an advanced ex vivo histology pipeline based on complementary 2-D (high-resolution semithin and ultrathin sectioning) and 3-D (CLARITY) techniques. Our goal is to fuse gold-standard ex vivo histology with MRI to validate the proposed model at central junctions of long-range fiber pathways within the well characterized human voluntary motor control network. If successful, we expect a paradigm shift in MRI-based computational models for in vivo tractography.
The successful applicant
should have a Master’s degree (or equivalent) in the disciplines neuroscience or biomedical sciences (medicine, biology, bioinformatics, biomedical engineering, or a comparable subject). A sound background in neuroanatomy and experience with histological techniques are an advantage. Proficiency in spoken and written English is mandatory.

Remuneration is based on the payscale of the Max Planck Society. The Max Planck Society is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals.

To apply, please submit a cover letter stating personal qualifications and motivation for applying, a curriculum vitae, contact details of two referees, and copies of your academic certificates and publications (if available). Please submit your application via our online system at http://www.cbs.mpg.de/vacancies (using subject heading “PHD 25/17”).

Closing date for applications is 05.01.2018. For further details please contact PD Dr Stefan Geyer ([Email Address Removed]). For more information about the project please see https://mico-mri.github.io