Leiden University Student Repository

Oikonomeas Koppasis, Nikolaos (2019)

Automation of identification and transformation of fluorescence images in CLEM data post-processing

Master thesis | Physics (MSc)

We introduce an open source, freely available algorithm for automatic correlation of fluorescence and electron microscopy images in Correlative Light-Electron Microscopy (CLEM). With a minimal amount of manual input, two custom modules perform an automatic identification of the fluorescent nuclei and the watershed nucleus of a TEM image and hence calculate the necessary affine transformation for accurate correlation. The process can be performed on a group of pre-processed images and allows for an efficient solution around the data handling bottleneck encountered in the technique.

CLEM

Automation

fluorescence

post-processing

transformation

identification

Author

Oikonomeas Koppasis, Nikolaos

Faculty

Faculty of Science

Specialisation

Soft and Biological Matter Physics

Supervisors

Noort, John van

ECTS Credits

5

Language

en