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TiQuant Software (www.msysbio.com/tiquant)
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.Overview
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
.Contact
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If you have questions, problems or comments, please contact A. Friebel (friebel[at]izbi.uni-leipzig.de).
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.Features
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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
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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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.Download
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Windows (64 Bit)
Current version: 1.0.0
 Linux
Current version: 1.0.0
Current version: 1.0.0

 
.Selected references
2.

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.

1.

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

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