Multiscale visualisation and analysis of innate immune cell migration at sites of hypoxic inflammation in vivo

Principal investigators: Friedemann Kiefer, Benjamin Risse
Project number: CRC 1450 B04
Project term: 01/2021–12/2028

Access to molecular oxygen is essential for cell function and behaviour. Tools to measure this central parameter, in particular in vivo, are limited. We generate hypoxia reporter systems, which we use to understand the contribution of immune cells to acute and chronic hypoxia in cells, organs and entire organisms. For the automated analysis of the big data, which we derive with our reporter systems in large tissue volumes, we have developed dedicated deep learning pipelines. We extend and accompany the resulting massive imaging data by complementary annotation and supervision tools, which allows us to analyse hypoxia across scales. Our approach provides unprecedented insights into the dynamics and consequences of hypoxia and its connection to inflammation.

Blood vessels from the brain tissue of a mouse. This visualisation is based on images which were taken using lightsheet microscopy and show layers of a tissue sample (here a section of about 100 layers on 550 x 550 x 300 µm). To contrast the blood vessels, an adhesion molecule in their endothelial cells was stained. We merged the microscopy data into a 3D image on the computer and used the hysteresis thresholding method to segment the blood vessels, i.e. to digitally delineate them from other tissue regions. The image serves as a reference for new image processing methods utilising machine learning to improve segmentation.
© Daniel Beckmann/Benjamin Risse's research group, microscopy data by Nadine Bauer/Friedemann Kiefer's research group

Team

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Publications

The names of the principal investigators in our network have been bolded. Publications released prior to 2021, when funding for our network commenced, represent previous project-related work.