Opening for a 15- or 20 ECTS internship for university master students.
Fluorescence microscopes image biological tissue sections to which fluorescent markers have been applied at many distinct wavelengths. The markers bind to specific antigens (proteins) on the exterior of cells, and as such enable identification of different (tumor) cell types and states.
The process of transforming raw camera sensor images into the final product, a tissue micrograph that maps out the spatial distribution of a large number of identified cell types and proteins, comprises a complex series of (nonlinear) image corrections, sub-image stitching and computational (biological) context-aware transformations. An efficient and high-throughput solution is critical due to the huge amount of image data. The design of this image processing pipeline takes place at the exciting vertex of biology, optics, and computer science.
More concretely, the project may include the following:
- Literature studies into the state of the art of fluorescence microscopy image (pre)-processing.
- Design of a logical image processing pipeline that takes raw camera sensor images as its input and prepares, combines, and filters them towards identification of the fluorescent markers.
Examples of pipeline steps include:
- Linear transformations such as noise suppression, flat-field correction, background subtraction
- Optical aberration corrections, deconvolution with the Point Spread Function.
- Stitching of tissue sub-images into single whole-tissue micrograph.
- Exploration of techniques employing information theory and machine learning.
- Proof-of-concept implementation of processing pipeline. In principle, in the Python ecosystem.
- Evaluating the pipeline using the experimental microscope installation in our lab at the HTC.
Key facts
- Full-time, flexible start and end dates.
- Office and lab spaces at the High Tech Campus (HTC) in Eindhoven.
- You will work with a small but highly skilled and motivated team.
- Possibility to expand the internship into a graduation project.
- Job opportunities in case of mutually positive cooperation.
If you are excited, or would like to know more, do not hesitate to contact us!
