Hoehme Lab • Research group
Multicellular systems biology • Image analysis • Multiscale liver models
We are developing the software packages TiQuant and TiSim in close collaboration with the INRIA/IfADo joint research group for Multicellular Systems Biology.


Quantification of experimental images

TiSim / CellSys

Modeling and simulations of biological tissue


Construction of models based on experimental images

Quantification of experimental images

TiQuant is a modular software tool for efficient quantification of biological tissues based on volume data obtained by biomedical image modalities. It includes a number of versatile image and volume processing chains tailored to the analysis of different tissue types which have been experimentally verified. TiQuant implements a novel method for the reconstruction of three-dimensional surfaces of biological systems, data that often cannot be obtained experimentally but which is of utmost importance for tissue modelling in systems biology. TiQuant
If you have questions, problems or comments, please contact A. Friebel (friebel[at]izbi.uni-leipzig.de).
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  • Nuclei reconstruction
  • Sinusoid and vein reconstruction
  • Bile canaliculi reconstruction
  • Cell shape reconstruction
  • Necrotic region reconstruction
  • Analysis of sinusoidal and bile canaliculi networks
  • Analysis of cells
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.Copyright notice
The TiQuant software package is free for non-commercial usage and is supplied in the presented form (all warranties are excluded). If you use the software in your publications please cite reference [1]+[2] from the list below, if your publication is in the liver context, and reference [2] otherwise. You may not decompile, reverse engineer, disassemble, attempt to derive the source code of, modify, or create derivative works of the software.


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Windows (64 Bit)
Current version: 1.0.0
Current version: 1.0.0
Current version: 1.0.0

.Selected references

Friebel, A., Neitsch, J., Johann, T., Hammad, S., Hengstler, JG., Drasdo, D., Hoehme, S. (2015)

TiQuant: Software for tissue analysis, quantification and surface reconstruction.

Bioinformatics (Accepted). doi: 10.1093/bioinformatics/btv346

This reference should be used for citations.


Hammad, S., Hoehme, S.Friebel, A., von Recklinghausen, I., Othman, A., Begher-Tibbe, B., Reif, R., Godoy, P., Johann, T., Vartak, A., Golka, K., Bucur, P.O., Vibert, E., Marchan, R., Christ, B., Dooley, S., Meyer, C., Ilkavets, I., Dahmen, U., Dirsch, O., Böttger, J., Gebhardt, R., Drasdo, D., Hengstler, JG. (2014) 

Protocols for staining of bile canalicular and sinusoidal networks of human, mouse and pig livers, three-dimensional reconstruction and quantification of tissue microarchitecture by image processing and analysis. 

Archives of Toxicology, Vol. 88 (5), pp 1161-1183; doi:10.1007/s00204-014-1243-5