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  3. PhD Candidate 'Optimisation and evaluation of newly developed segmentation algorithms for 19F MRI'

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PhD Candidate 'Optimisation and evaluation of newly developed segmentation algorithms for 19F MRI'

Job describtion Objectives The task of ESR12 will be to develop image processing techniques and to develop novel algorithms for 19F MRI, as/since existing …

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Arbeidsvoorwaarden

Standplaats:
Albinusdreef, Leiden, Zuid-Holland
Dienstverband:
Tijdelijk contract / Tijdelijke opdracht
Uren per week:
36 uur
Salarisindicatie:
€ 2495 - € 3196 per maand
Opleidingsniveau:
WO

Functieomschrijving

Job describtion Objectives

The task of ESR12 will be to develop image processing techniques and to develop novel algorithms for 19F MRI, as/since existing semi-automated image segmentation techniques need to be adapted to extract quantitative 2D and 3D imaging data. A multi-atlas 3D segmentation technique will be developed, which can perform automated and unsupervised segmentation of the area-of-interest. Similar approaches were previously considered as not viable since conventional multislice 2D imaging suffered from highly anisotropic resolution with in-plane and through-plane misalignment of acquired 2D slices. Automated image registration and label-fusion will now be used to segment new unseen data. Both 3D and 3D-plus-time registration will be investigated. As 3D registration is computationally demanding, the proposed fully automated segmentation approach can only be applied when offline image analysis is considered acceptable. Additionally, the approach may not be sufficiently reliable for patients with distinct anatomical abnormalities. Therefore, a user-guided segmentation approach is proposed. A user-defined 3D segmentation approach that requires manual user-input will also be developed. Such user-input can be used to indicate for instance the approximate size of the area-of-interest or to indicate the exact position of specific anatomical landmarks within the area-of-interest to guide segmentation. Combining user-interaction with a real-time updating segmentation may then serve in the future as a clinically viable solution in challenging cases, such as in patients with abnormal anatomy.

Expected Results

The goal of this work package is to develop and evaluate new methods for accurate segmentation of the area of interest (i.e. liver, cardiac structures, vascular territories, etc.) and to obtain quantitative imaging biomarkers within the segmented area-of-interest. Optimisation and evaluation of the newly developed segmentation algorithms will be performed using clinically obtained data. Once an accurate segmentation of the structures of interest is obtained, 3D registration techniques can be employed to transfer a defined segmentation between all available sequences. For segmentation purposes, both user-guided, semi-automated segmentation techniques as well as fully automated atlas-based segmentation algorithms will be developed and evaluated in this work package.

Planned secondments

To POLY for 3 months (m29-31) to learn about 3D segmentation techniques. To UCIT for 2 months (m12-13) to learn different 19F MRI applications. To PROG for 2 months (m22-23) for business plan writing and exploitation of MED results.

Functie-eisen

You hold a degree from a Technical University in Technical Medicine or Physics. The position is staffed at Medres Germany. The LUMC is the PhD academic awarding centre. To be eligible for this ESR position, you must NOT have worked in Germany for more than 12 months in total over the period of the last three years prior to joining NOVA-MRI. To be eligible for this position, it is ususally a person living outside of Germany (can be both inside and outside of the EU).

Conditions

As a PhD candidate, you will be appointed for the duration of three years. Your salary is a maximum of € 2,422 in the first year, amounting to a maximum of € 3,103 in the final year (scale PhD students, Collective Labour Agreement University Medical Centers).