Deutsch Intern
Rudolf Virchow Center for Integrative and Translational Bioimaging

Anne Auer

With my background in Biomedicine, Bioinformatics, and Microscopy, I joined the Heinze Lab in September 2022 for my doctoral thesis. The goal of my thesis is to develop an imaging pipeline for the detection of B cells in mouse hearts in the context of myocardial infarction with light sheet fluorescent microscopy. My work is part of a ‘Sonderforschungsbereich’ to better understand the cardio-immune interface, a growing field between cardiology and biomedicine.

My project includes sample preparation for light sheet microscopy, imaging with different microscopy modalities, and the analysis of the high content fluorescent images. To be able to image whole organs with light sheet microscopy, the scattering of the sample must be reduced by clearing the tissue until it becomes transparent. There are various methods and protocols available, and one part of my project is to find the optimal protocol for the clearing of mouse hearts which are stained with fluorescent proteins. Confocal microscopy and light sheet fluorescent microscopy are the standard methods of the project, but I have also operated RESOLFT and STED microscopy set-ups before my time in Würzburg. For the analysis of high content fluorescent images, several algorithms and software will be combined to create high quality images and movies of whole mouse organs. Spectral unmixing algorithms will play an important role since the more fluorophores are used for high content imaging, the more the emission spectra of the fluorophores can overlap.  Spectral unmixing is separating the emission of the fluorophores computationally by reducing the cross-talk from one detection channel to another.