Hoehme – Image analysis and multiscale tissue modeling


Research interests

Our research is part of the search for understanding of the integrated physiological function of the human body in terms of structure and function of tissues, cells and proteins. Currently, we are focussing on two main objectives:

  • Technological advancement (novel algorithms, advanced programming and parallelization techniques etc.) for image processing and analysis, and 3D tissue modelling.
  • Automatization and standardization of creation of individual-cell-based spatio-temporal multi-scale models for biological tissues directly from experimental image modalities.
  • Application of these tissue models to elucidate the mechanisms behind liver regeneration after intoxication and partial liver resection in different species to better understand liver failure in human.


  • French National Institute for Research in Computer Science and Control (INRIA) in Paris, France >>>
  • Leibniz Research Centre for Working Environment and Human Factors (IfaDo) in Dortmund, Germany >>>
  • Helmholtz German Cancer Research Center (DKFZ) in Heidelberg, Germany >>>
  • Auckland Bioengineering Institute (ABI) in Auckland, New Zealand >>>
  • University College (UCL) in London, United Kingdom >>>
  • Chalmers University of Technology in Gothenburg, Sweden >>>
  • Molecular hepatology, University Hospital Mannheim, University of Heidelberg in Mannheim, Germany >>>
  • Fraunhofer Institute for Medical Image Computing (MEVIS) in Bremen,Germany >>>
  • Institute for Biochemistry, Medical Faculty, University of Leipzig >>>
  • Image and Signal Processing Group at the Department of Computer Science (IfI) University of Leipzig >>>
  • Bioinformatics Group at the Department of Computer Science, University of Leipzig >>>

follow our group here: https://hoehmelab.izbi.uni-leipzig.de/



2023 (3)

  • R. J. P. Custodio, Z. Hobloss, M. Myllys, R. Hassan, D. González, J. Reinders, J. Bornhorst, A. K. Weishaupt, A. L. Seddek, T. Abbas, A. Friebel, S. Hoehme, S. Getzmann, J. G. Hengstler, C. van Thriel, A. Ghallab. Cognitive Functions, Neurotransmitter Alterations, and Hippocampal Microstructural Changes in Mice Caused by Feeding on Western Diet. Cells. 2023. 12:
  • A. Ghallab, D. González, E. Strängberg, U. Hofmann, M. Myllys, R. Hassan, Z. Hobloss, L. Brackhagen, B. Begher-Tibbe, J. C. Duda, C. Drenda, F. Kappenberg, J. Reinders, A. Friebel, M. Vucur, M. Turajski, A. L. Seddek, T. Abbas, N. Abdelmageed, S. A. F. Morad, W. Morad, A. Hamdy, W. Albrecht, N. Kittana, M. Assali, N. Vartak, C. van Thriel, A. Sous, P. Nell, M. Villar-Fernandez, C. Cadenas, E. Genc, R. Marchan, T. Luedde, P. Åkerblad, J. Mattsson, H. U. Marschall, S. Hoehme, G. Stirnimann, M. Schwab, P. Boor, K. Amann, J. Schmitz, J. H. Bräsen, J. Rahnenführer, K. Edlund, S. J. Karpen, B. Simbrunner, T. Reiberger, M. Mandorfer, M. Trauner, P. A. Dawson, E. Lindström, J. G. Hengstler. Inhibition of the renal apical sodium dependent bile acid transporter prevents cholemic nephropathy in mice with obstructive cholestasis. J Hepatol. 2023. 80: 268-281.
  • Stefan Hoehme, Seddik Hammad, Jan Boettger, Brigitte Begher-Tibbe, Petru Bucur, Eric Vibert, Rolf Gebhardt, Jan G. Hengstler, Dirk Drasdo. Digital twin demonstrates significance of biomechanical growth control in liver regeneration after partial hepatectomy. iScience. 2023. 26: 105714.

2022 (6)

  • A. Friebel, T. Johann, D. Drasdo, S. Hoehme. Guided interactive image segmentation using machine learning and color-based image set clustering. Bioinformatics. 2022. 38: 4622-4628.
  • A. Ghallab, R. Hassan, U. Hofmann, A. Friebel, Z. Hobloss, L. Brackhagen, B. Begher-Tibbe, M. Myllys, J. Reinders, N. Overbeck, S. Sezgin, S. Zühlke, A. L. Seddek, W. Murad, T. Brecklinghaus, F. Kappenberg, J. Rahnenführer, D. González, C. Goldring, I. M. Copple, R. Marchan, T. Longerich, M. Vucur, T. Luedde, S. Urban, A. Canbay, T. Schreiter, M. Trauner, J. Y. Akakpo, M. Olyaee, S. C. Curry, J. P. Sowa, H. Jaeschke, S. Hoehme, J. G. Hengstler. Interruption of bile acid uptake by hepatocytes after acetaminophen overdose ameliorates hepatotoxicity. J Hepatol. 2022. 77: 71-83.
  • R. Hassan, A. Friebel, L. Brackhagen, Z. Hobloss, M. Myllys, D. González, W. Albrecht, E. S. I. Mohammed, A. L. Seddek, R. Marchan, C. Cadenas, B. Cramer, H. U. Humpf, L. Hartl, B. Simbrunner, T. Reiberger, M. Trauner, S. Hoehme, G. H. Degen, J. G. Hengstler, A. Ghallab. Hypoalbuminemia affects the spatio-temporal tissue distribution of ochratoxin A in liver and kidneys: consequences for organ toxicity. Arch Toxicol. 2022. 96: 2967-2981.
  • R. Hassan, D. González, Z. Hobloss, L. Brackhagen, M. Myllys, A. Friebel, A. L. Seddek, R. Marchan, B. Cramer, H. U. Humpf, S. Hoehme, G. H. Degen, J. G. Hengstler, A. Ghallab. Inhibition of cytochrome P450 enhances the nephro- and hepatotoxicity of ochratoxin A. Arch Toxicol. 2022. 96: 3349-3361.
  • R. Hassan, M. Myllys, L. Brackhagen, Z. Hobloss, D. González, A. L. Seddek, A. Friebel, S. Hoehme, R. Marchan, M. Trauner, J. G. Hengstler, A. Ghallab. Colchicine overdose impairs the capacity of Kupffer cells to clear foreign particles and endotoxins. Arch Toxicol. 2022. 96: 3067-3076.
  • Christian H. Holland, Ricardo O. Ramirez Flores, Maiju Myllys, Reham Hassan, Karolina Edlund, Ute Hofmann, Rosemarie Marchan, Cristina Cadenas, Jörg Reinders, Stefan Hoehme, Abdel-latif Seddek, Steven Dooley, Verena Keitel, Patricio Godoy, Brigitte Begher-Tibbe, Christian Trautwein, Christian Rupp, Sebastian Mueller, Thomas Longerich, Jan G. Hengstler, Julio Saez-Rodriguez, Ahmed Ghallab. Transcriptomic Cross-Species Analysis of Chronic Liver Disease Reveals Consistent Regulation Between Humans and Mice. Hepatology Communications. 2022. 6: 161-177.

2021 (3)

  • A. Ghallab, R. Hassan, M. Myllys, W. Albrecht, A. Friebel, S. Hoehme, U. Hofmann, A. L. Seddek, A. Braeuning, L. Kuepfer, B. Cramer, H. U. Humpf, P. Boor, G. H. Degen, J. G. Hengstler. Subcellular spatio-temporal intravital kinetics of aflatoxin B(1) and ochratoxin A in liver and kidney. Arch Toxicol. 2021. 95: 2163-2177.
  • Ahmed Ghallab, Maiju Myllys, Adrian Friebel, Julia Duda, Karolina Edlund, Emina Halilbasic, Mihael Vucur, Zaynab Hobloss, Lisa Brackhagen, Brigitte Begher-Tibbe, Reham Hassan, Michael Burke, Erhan Genc, Lynn Johann Frohwein, Ute Hofmann, Christian H. Holland, Daniela González, Magdalena Keller, Abdel-latif Seddek, Tahany Abbas, Elsayed S. I. Mohammed, Andreas Teufel, Timo Itzel, Sarah Metzler, Rosemarie Marchan, Cristina Cadenas, Carsten Watzl, Michael A. Nitsche, Franziska Kappenberg, Tom Luedde, Thomas Longerich, Jörg Rahnenführer, Stefan Hoehme, Michael Trauner, Jan G. Hengstler. Spatio-Temporal Multiscale Analysis of Western Diet-Fed Mice Reveals a Translationally Relevant Sequence of Events during NAFLD Progression. Cells. 2021. 10: 2516.
  • N. Vartak, G. Guenther, F. Joly, A. Damle-Vartak, G. Wibbelt, J. Fickel, S. Jörs, B. Begher-Tibbe, A. Friebel, K. Wansing, A. Ghallab, M. Rosselin, N. Boissier, I. Vignon-Clementel, C. Hedberg, F. Geisler, H. Hofer, P. Jansen, S. Hoehme, D. Drasdo, J. G. Hengstler. Intravital Dynamic and Correlative Imaging of Mouse Livers Reveals Diffusion-Dominated Canalicular and Flow-Augmented Ductular Bile Flux. Hepatology. 2021. 73: 1531-1550.

2018 (1)

  • G. Peeters, C. Debbaut, A. Friebel, P. Cornillie, W. H. De Vos, K. Favere, I. Vander Elst, T. Vandecasteele, T. Johann, L. Van Hoorebeke, D. Monbaliu, D. Drasdo, S. Hoehme, W. Laleman, P. Segers. Quantitative analysis of hepatic macro- and microvascular alterations during cirrhogenesis in the rat. J Anat. 2018. 232: 485-496.

2017 (1)

  • S. Hoehme, A. Friebel, S. Hammad, D. Drasdo, J. G. Hengstler. Creation of Three-Dimensional Liver Tissue Models from Experimental Images for Systems Medicine. Methods Mol Biol. 2017. 1506: 319-362.

2016 (1)

  • A. Ghallab, G. Celliere, S. G. Henkel, D. Driesch, S. Hoehme, U. Hofmann, S. Zellmer, P. Godoy, A. Sachinidis, M. Blaszkewicz, R. Reif, R. Marchan, L. Kuepfer, D. Haussinger, D. Drasdo, R. Gebhardt, J. G. Hengstler. Model-guided identification of a therapeutic strategy to reduce hyperammonemia in liver diseases. J Hepatol. 2016. 64: 860-71.