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

Principal investigators

Project members

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.

2025

Kunisch M, Beutler S, Pilger C, Kiefer F, Huser T, Wirth B. Active axial motion compensation in multiphoton-excited fluorescence microscopy. Opt Express 2025;33: 3620-3636. Abstract

2024

Bauer N, Beckmann D, Reinhardt D, Frost N, Bobe S, Erapaneedi R, Risse B, Kiefer F. Therapy-induced modulation of tumor vasculature and oxygenation in a murine glioblastoma model quantified by deep learning-based feature extraction. Sci Rep 2024;14: 2034. Abstract
Bauer N, Kiefer F. Genetically Encoded Reporters to Monitor Hypoxia. Methods Mol Biol 2024;2755: 3-29. Abstract
Haalck L, Thiele S, Risse B. Tracking Tiny Insects in Cluttered Natural Environments Using Refinable Recurrent Neural Networks. IEEE/CVF Winter Conference 2024: 7126-7135. Abstract

2023

Bauer N, Maisuls I, Pereira da Graca A, Reinhardt D, Erapaneedi R, Kirschnick N, Schäfers M, Grashoff C, Landfester K, Vestweber D, Strassert CA, Kiefer F. Genetically encoded dual fluorophore reporters for graded oxygen-sensing in light microscopy. Biosens Bioelectron 2023;221: 114917. Abstract
Beckmann D, Kockwelp J, Gromoll J, Kiefer F, Risse B. SAM meets Gaze: Passive Eye Tracking for Prompt-based Instance Segmentation. NeuRIPS. 2023 Workshop on Gaze Meets ML 2023
Haalck L, Mangan M, Wystrach A, Clement L, Webb B, Risse B. CATER: Combined Animal Tracking & Environment Reconstruction. Sci Adv 2023;9: eadg2094. Abstract
Kockwelp J, Gromoll J, Wistuba J, Risse B. EyeGuide-From Gaze Data to Instance Segmentation. British Machine Vision Conference BMVC. 2023
Kockwelp J, Thiele S, Kockwelp P, Bartsch J, Schliemann C, Angenendt L, Risse B. Cell Selection-based Data Reduction Pipeline for Whole Slide Image Analysis of Acute Myeloid Leukemia. 2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) 2023: 1824-1833. Abstract

2022

Bobe S, Beckmann D, Klump DM, Dierkes C, Kirschnick N, Redder E, Bauer N, Schäfers M, Erapaneedi R, Risse B, van de Pavert SA, Kiefer F. Volumetric imaging reveals VEGF-C-dependent formation of hepatic lymph vessels in mice. Front Cell Dev Biol 2022;10: 949896. Abstract
Eliat F, Sohn R, Renner H, Kagermeier T, Volkery S, Brinkmann H, Kirschnick N, Kiefer F, Grabos M, Becker K, Bedzhov I, Schöler HR, Bruder JM. Tissue clearing may alter emission and absorption properties of common fluorophores. Sci Rep 2022;12: 5551. Abstract
Peil J, Bock F, Kiefer F, Schmidt R, Heindl LM, Cursiefen C, Schlereth SL. New Therapeutic Approaches for Conjunctival Melanoma-What We Know So Far and Where Therapy Is Potentially Heading: Focus on Lymphatic Vessels and Dendritic Cells. Int J Mol Sci 2022;23Abstract
Reimche I, Yu H, Ariantari NP, Liu Z, Merkens K, Rotfuß S, Peter K, Jungwirth U, Bauer N, Kiefer F, Neudörfl J-M, Schmalz H-G, Proksch P, Teusch N. Phenanthroindolizidine Alkaloids Isolated from Tylophora ovata as Potent Inhibitors of Inflammation, Spheroid Growth, and Invasion of Triple-Negative Breast Cancer. Int J Mol Sci 2022;23Abstract

2021

Arasa J, Collado-Diaz V, Kritikos I, Medina-Sanchez JD, Friess MC, Sigmund EC, Schineis P, Hunter MC, Tacconi C, Paterson N, Nagasawa T, Kiefer F, Makinen T, Detmar M, Moser M, Lämmermann T, Halin C. Upregulation of VCAM-1 in lymphatic collectors supports dendritic cell entry and rapid migration to lymph nodes in inflammation. J Exp Med 2021;218Abstract
Bian A, Jiang X, Berh D, Risse B. Resolving Colliding Larvae by Fitting ASM to Random Walker-Based Pre-Segmentations. IEEE/ACM Trans Comput Biol Bioinform 2021;18: 1184-1194. Abstract
Huesmann K, Rodriguez LG, Linsen L, Risse B. The Impact of Activation Sparsity on Overfitting in Convolutional Neural Networks. Pattern Recognition. ICPR International Workshops and Challenges 2021: 130-145. Abstract
Kirschnick N, Drees D, Redder E, Erapaneedi R, Pereira da Graca A, Schäfers M, Jiang X, Kiefer F. Rapid methods for the evaluation of fluorescent reporters in tissue clearing and the segmentation of large vascular structures. iScience 2021;24: 102650. Abstract
Kong C, Bobe S, Pilger C, Lachetta M, Øie CI, Kirschnick N, Mönkemöller V, Hübner W, Förster C, Schüttpelz M, Kiefer F, Huser T, Schulte Am Esch J. Multiscale and Multimodal Optical Imaging of the Ultrastructure of Human Liver Biopsies. Front Physiol 2021;12: 637136. Abstract
Redder E, Kirschnick N, Bobe S, Hägerling R, Hansmeier NR, Kiefer F. Vegfr3-tdTomato, a reporter mouse for microscopic visualization of lymphatic vessel by multiple modalities. PLoS One 2021;16: e0249256. Abstract
Sadras T, Martin M, Kume K, Robinson ME, Saravanakumar S, Lenz G, Chen Z, Song JY, Siddiqi T, Oksa L, Knapp AM, Cutler J, Cosgun KN, Klemm L, Ecker V, Winchester J, Ghergus D, Soulas-Sprauel P, Kiefer F, Heisterkamp N, Pandey A, Ngo V, Wang L, Jumaa H, Buchner M, Ruland J, Chan W-C, Meffre E, Martin T, Müschen M. Developmental partitioning of SYK and ZAP70 prevents autoimmunity and cancer. Mol Cell 2021;81: 2094-2111.e9. Abstract

2018

Hägerling R, Hoppe E, Dierkes C, Stehling M, Makinen T, Butz S, Vestweber D, Kiefer F. Distinct roles of VE‐cadherin for development and maintenance of specific lymph vessel beds. EMBO J 2018: e98271. Abstract
Klemm S, Jiang X, Risse B. Deep distance transform to segment visually indistinguishable merged objects. In: Proc. of 40th German Conference on Pattern Recognition (GCPR), Stuttgart 2018: 422-433.
Orlich M, Kiefer F. A qualitative comparison of ten tissue clearing techniques. Histol Histopathol 2018;33: 181-199. Abstract

2017

Hägerling R, Drees D, Scherzinger A, Dierkes C, Martin-Almedina S, Butz S, Gordon K, Schäfers M, Hinrichs K, Ostergaard P, Vestweber D, Goerge T, Mansour S, Jiang X, Mortimer PS, Kiefer F. VIPAR, a quantitative approach to 3D histopathology applied to lymphatic malformations. JCI Insight 2017;2: e93424. Abstract

2016

Erapaneedi R, Belousov VV, Schäfers M, Kiefer F. A novel family of fluorescent hypoxia sensors reveal strong heterogeneity in tumor hypoxia at the cellular level. Embo J 2016;35: 102-113. Abstract