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Type: Internship
Name (ID): Experimental validation of 3D micro-flow estimation methods (OP-20190715-162156)
Supervised by: Michael LIEBLING


Pulsatile flow patterns play an important role during development of the vertebrate circulatory system, in particular, the heart. Optical sectioning microscopy offers the possibility of imaging sections within developing embryos or larvae of animal models such as the zebrafish at high speed but imaging flow, which is inherently 3D, remains challenging. Several techniques have been proposed that build upon the assumption of a repetitive flow to record rapid image series at increasing (static) depths and, possibly orientations. However, the characterization and practical validation of these techniques remains superficial.

The aim of this project is to develop an experimental pulsatile flow characterization setup that can be combined with an existing light-sheet fluorescence microscopy system and evaluate the quality of computational flow estimation methods.

Specifically, the tasks are: 1. develop a simple, orientable, micro-fluidic channel (tubing) to produce controlled pulsatile 2D flow patterns that can be inspected (under variable orientations) in an existing light-sheet microscope (open-SPIM), 2. acquire image series, 3. apply existing and/or new flow analysis methods, to be selected among optical flow, DPIV, PatchMatch or other flow estimation methods.

Candidate should have prior experience with microscopy, image processing, and micro-fluidics. This 6-month project is suitable as an external MS project.

About Idiap:

Idiap is an independent, not-for-profit, research institute recognized and funded by the Swiss Federal Government, the State of Valais, and the City of Martigny.

Idiap offers competitive salaries and conditions at all levels in a young, high-quality, dynamic, and multicultural environment. Idiap is an equal opportunity employer and is actively involved in the "Advancement of Women in Science" European initiative. The Institute seeks to maintain a principle of open competition (on the basis of merit) to appoint the best candidate, provides equal opportunity for all candidates, and equally encourage both genders to apply.

Idiap is located in the town of Martigny in Valais, a scenic region in the south of Switzerland, surrounded by the highest mountains of Europe, and offering exceptional quality of life, exciting recreational activities, including hiking, climbing and skiing, as well as varied cultural activities. It is within close proximity to Lausanne and Geneva. Although Idiap is located in the French part of Switzerland, English is the official working language. Free French lessons are also provided on a complimentary basis.

For frequently asked questions (FAQs) about living in Switzerland, please go to

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