Computational and Mathematical Methods in Medicine
Volume 2012 (2012), Article ID 128431, 8 pages
Research Article

Quantitative Measurements in 3-Dimensional Datasets of Mouse Lymph Nodes Resolve Organ-Wide Functional Dependencies

1EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader 88, 08003 Barcelona, Spain
2Theodor Kocher Institut, Universität Bern, Freiestrasse 1, 3012 Bern, Switzerland

Received 1 June 2012; Accepted 13 August 2012

Academic Editor: Huafeng Liu

Copyright © 2012 Jürgen Mayer et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Deep tissue imaging has become state of the art in biology, but now the problem is to quantify spatial information in a global, organ-wide context. Although access to the raw data is no longer a limitation, the computational tools to extract biologically useful information out of these large data sets is still catching up. In many cases, to understand the mechanism behind a biological process, where molecules or cells interact with each other, it is mandatory to know their mutual positions. We illustrate this principle here with the immune system. Although the general functions of lymph nodes as immune sentinels are well described, many cellular and molecular details governing the interactions of lymphocytes and dendritic cells remain unclear to date and prevent an in-depth mechanistic understanding of the immune system. We imaged ex vivo lymph nodes isolated from both wild-type and transgenic mice lacking key factors for dendritic cell positioning and used software written in MATLAB to determine the spatial distances between the dendritic cells and the internal high endothelial vascular network. This allowed us to quantify the spatial localization of the dendritic cells in the lymph node, which is a critical parameter determining the effectiveness of an adaptive immune response.