Only little is known about how cells coordinately behave to establish functional tissue structure and restore microarchitecture during regeneration. Research in this field is hampered by a lack of techniques that allow quantification of tissue architecture and its development. To bridge this gap, we have established a procedure based on confocal laser scans, image processing, and three-dimensional tissue reconstruction, as well as quantitative mathematical modeling. As a proof of principle, we reconstructed and modeled liver regeneration in mice after damage by CCl(4), a prototypical inducer of pericentral liver damage. We have chosen the regenerating liver as an example because of the tight link between liver architecture and function: the complex microarchitecture formed by hepatocytes and microvessels, i.e. sinusoids, ensures optimal exchange of metabolites between blood and hepatocytes. Our model captures all hepatocytes and sinusoids of a liver lobule during a 16 day regeneration process. The model unambiguously predicted a so-far unrecognized mechanism as essential for liver regeneration, whereby daughter hepatocytes align along the orientation of the closest sinusoid, a process which we named ''hepatocytesinusoid alignment" (HSA). The simulated tissue architecture was only in agreement with the experimentally obtained data when HSA was included into the model and, moreover, no other likely mechanism could replace it. In order to experimentally validate the model of prediction of HSA, we analyzed the three-dimensional orientation of daughter hepatocytes in relation to the sinusoids. The results of this analysis clearly confirmed the model prediction. We believe our procedure is widely applicable in the systems biology of tissues.Ó 2010 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.Multiple studies have been performed to understand the molecular mechanisms involved in the regulation of liver regeneration [1]. However, little is known regarding the changes in the threedimensional organization of the liver's microarchitecture occurring during this process. These changes may be critical in determining whether a certain type of injury will result in liver regeneration or scar formation. In the excellent manuscript by Hoehme et al.[2] the authors used immunostaining, fluorescent reporter mice, confocal microscopy, and computer/mathematical modeling to develop a model that predicts how hepatic microarchitecture is re-established after acute CCl 4 -induced liver damage. The results support a process that includes transient loss of polarity and increased migration by recently replicated hepatocytes which allow the daughter hepatocytes to quickly align along the closest hepatic sinusoids. The authors term this process hepatocyte sinusoidal alignment (HSA) and conclude that recovery of normal hepatic microarchitecture (i.e., regeneration) is not achieved unless an HSA occurs. These results stress the fact that cell-cell and cell-matrix interactions are critical for the...