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Section: New Software and Platforms
TiQuant
Tissue Quantifier
Keywords: Systems Biology - Bioinformatics - Biology - Physiology
Systems biology and medicine on histological scales require quantification of images from histological image modalities such as confocal laser scanning or bright field microscopy. The latter can be used to calibrate the initial state of a mathematical model, and to evaluate its explanatory value, which hitherto has been little recognised. We generated a software for image analysis of histological material and demonstrated its use in analysing liver confocal micrografts, called TiQuant (Tissue Quantifier). The software is part of an analysis chain detailing protocols of imaging, image processing and analysis in liver tissue, permitting 3D reconstructions of liver lobules down to a resolution of less than a micrometer [72]. It is implemented in portable object-oriented ANSI C. The GUI is based on QT and supports real-time visualisation using OpenGL. TiQuant is embedded in the tissue modelling framework CellSys and thus is tightly linked with TiSim, a versatile and efficient simulation environment for tissue models. TiQuant provides an interface to VolView and further complements its functionality by linking to the open-source libraries ITK and VTK (itk/vtk.org). The image/volume processing chains currently implemented in TiQuant for example include techniques to segment conduit and cell segmentation from 3D confocal micrographs of liver tissue based on the Adaptive Otsu Thresholding method and a number of morphological operators [75]. TiQuant is currently extended by a machine learning component.
Functional Description
We generated a software for image analysis of histological material and demonstrated its use in analysing liver confocal micrografts, called TiQuant (Tissue Quantifier). The software is part of an analysis chain detailing protocols of imaging, image processing and analysis in liver tissue, permitting 3D reconstructions of liver lobules down to a resolution of less than a micrometer.