Skip to content

To obtain a holistic image of the molecular mechanisms in the cells, for example inflammatory responses or rejection reactions after transplantation, it is necessary to analyse biological structures from the level of the entire organ down to the nano level. For this purpose, researchers on the »Imaging of Large Tissues« project are developing a workflow to combine the various microscopy imaging methods and analytical, mass spectroscopy methods. This approach facilitates more comprehensive, more precise and more resource-conserving analyses of biological and clinical samples.

The project’s objective is to obtain from one and the same sample more information on the cellular composition and the functional interactions. This is essential to achieve a more precise diagnosis or to identify therapeutic targets. The techniques employed such as light sheet fluorescence microscopy, confocal microscopy and mass spectrometry make it possible to examine tissue ranging from the level of entire organs and individual cells right down to molecular structures. This would not be technically feasible using each technique individually; only by combining all the above methods does it become possible to examine simultaneously the various orders of magnitude of which tissue is composed – and to understand the interaction between anatomy and functioning.

Insights into cellular mechanisms in rejection reactions of transplanted organs

For the research project, the researchers are trialling the workflow using murine (from mice) and human kidneys. The samples originate from the Department of General, Visceral and Vascular Surgery at the Charité University Hospital in Berlin.

To date, the cellular mechanisms that lead to rejection reactions of transplanted organs have been poorly understood. Even the influence of how the organ is transported (refrigerated, perfused, stored at 37 °C body temperature) is still unclear. The »Imaging of Large Tissues« project therefore also aims to uncover the inflammatory mechanisms underlying the rejection reactions after kidney transplants. In this way, the researchers intend to identify approaches to treat rejection reactions as well as diagnostic parameters to assess whether an organ is suitable for transplant.


Select publications

Cell Reports Methods, Vol. 3, No. 3, 2023, P. 100436

Spangenberg P, Hagemann N, Squire A, Förster N, Krauß SD, Qi Y, Mohamud Yusuf A, Wang J, Grüneboom A, Kowitz L, Korste S, Totzeck M, Cibir Z, Tuz AA,…

Rapid and fully automated blood vasculature analysis in 3D light-sheet image volumes of different organs

Immunological Reviews, Vol. 306, No. 1, 2021, P. 293-303

Grüneboom A, Aust O, Cibir Z, Weber F, Hermann DM, Gunzer M.

Imaging innate immunity

Cells, Vol. 10, No. 12, 2021

Della Marina A, Arlt A, Schara-Schmidt U, Depienne C, Gangfuß A, Kölbel H, Sickmann A, Freier E, Kohlschmidt N, Hentschel A, Weis J, Czech AA,…

Phenotypical and Myopathological Consequences of Compound Heterozygous Missense and Nonsense Variants in SLC18A3

Immunity, Vol. 54, No. 11, 2021, P. 2531-2546.e5

Faas M, Ipseiz N, Ackermann J, Culemann S, Grüneboom A, Schröder F, Rothe T, Scholtysek C, Eberhardt M, Böttcher M, Kirchner P, Stoll C, Ekici A,…

IL-33-induced metabolic reprogramming controls the differentiation of alternatively activated macrophages and the resolution of inflammation

Immunity, Vol. 54, No. 5, 2021, P. 1002-1021.e10

Friščić J, Böttcher M, Reinwald C, Bruns H, Wirth B, Popp S, Walker KI, Ackermann JA, Chen X, Turner J, Zhu H, Seyler L, Euler M, Kirchner P, Krüger…

The complement system drives local inflammatory tissue priming by metabolic reprogramming of synovial fibroblasts

The Ocular Surface, Vol. 20, No. 20, 2021, P. 1-12

Mahajan A, Hasíková L, Hampel U, Grüneboom A, Shan X, Herrmann I, Garreis F, Bock F, Knopf J, Singh J, Schauer C, Mahajan S, Leppkes M, Paulsen F,…

Aggregated neutrophil extracellular traps occlude Meibomian glands during ocular surface inflammation

Theranostics, Vol. 11, No. 6, 2021, P. 2876-2891

Schneidereit D, Bröllochs A, Ritter P, Kreiß L, Mokhtari Z, Beilhack A, Krönke G, Ackermann JA, Faas M, Grüneboom A, Schürmann S, Friedrich O.

An advanced optical clearing protocol allows label-free detection of tissue necrosis via multiphoton microscopy in injured whole muscle

Further projects

3D Molecular Pathology

The aim of the work carried out by researchers in the »3D molecular pathology« project is to gain a better understanding of the influence of inflammatory cells on the course of diseases that trigger massive immune reactions.

Biochemical Annotations of Mass Spectrometry Imaging Data for Worldwide Exchange

The research groups AMBIOM and Spatial Metabolomics are working together to develop a plug-in for the multi-dimensional imaging software napari that makes it possible to visualise and biochemically annotate MSI data.

Creating 'Leibniz Mass Spectral Imaging Library' for Identification of Primary & Secondary Metabolites

The project aims at creating the first-ever open-access MSI library of over 1000 bioactive compound standards on different matrix-assisted laser desorption/ionization (MALDI) MSI platforms.

Synthesis, Structure & Biological Effects of Ultrasmall (1–2 nm) Bimetallic Silver-Platinum Nanoparticles

In the »Synthesis, Structure & Biological Effects of Ultrasmall (1–2 nm) Bimetallic Silver-Platinum Nanoparticles« project, ISAS researchers are examining the antimicrobial activities of nanoparticles.

TRR 332 – Neutrophil Granulocytes: Development, Behaviour & Function

At ISAS, scientists in the subproject »Phagocytic crosstalk between neutrophils and macrophages« investigate how immune cells of the type of phagocytes – in specific neutrophil granulocytes and macrophages – communicate with one another.

Smart Human-in-the-loop Segmentation

Scientist working on the project »Smart Human-in-the-loop Segmentation« aim to develop a powerful deep learning model that is trained with a minimum amount of human effort.

Cell Tracking in Microscopy Images

The research project »Cell Tracking in Microscopy Images« aims to develop new sophisticated cell detection and tracking algorithms to tackle some of the most challenging tracking problems.

Chemical Probes

The goal of the project »Chemical Probes« is to gain insight into the importance of these processes in biomedical questions using a chemical proteomics approach.