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Section: New Software and Platforms
TiQuant
Tissue Quantifier
Keywords: Systems Biology - Bioinformatics - Biology - Physiology
Functional Description
Systems biology and medicine on histological scales require the 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 has been little recognised thus far. 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, allowing 3D reconstructions of liver lobules down to a resolution of less than a micrometer. The software has been made available to the public by publication in ref. [14] , together with a new surface reconstruction algorithm based on the morphological Watershed algorithm. We validated that this algorithm allows reconstruction of cell shapes from nucleus and blood microvessel information, and demonstrated that it allows a reliable estimate of liver lobules, the smallest repetitive functional and micro-anatomical liver units, that besides in pig are not anatomically separated.
A separate 2D version of it (TI-Quant-BF-2D) has been used to analyse the invasion pattern of non-small cell lung cancer (NSCLC) cells in vitro [24] (see below).