Abstract
Due to their involvement in many physiologic and pathologic processes, there is a great interest in identifying new molecular pathways that mediate the formation and function of blood and lymphatic vessels. Vascular research increasingly involves the image-based analysis and quantification of vessel networks in tissue whole-mounts or of tube-like structures formed by cultured endothelial cells in vitro. While both types of experiments deliver important mechanistic insights into (lymph)angiogenic processes, the manual analysis and quantification of such experiments are typically labour-intensive and affected by inter-experimenter variability. To bypass these problems, we developed AutoTube, a new software that quantifies parameters like the area covered by vessels, vessel width, skeleton length and branching or crossing points of vascular networks in tissues and in in vitro assays. AutoTube is freely downloadable, comprises an intuitive graphical user interface and helps to perform otherwise highly time-consuming image analyses in a rapid, automated and reproducible manner. By analysing lymphatic and blood vascular networks in whole-mounts prepared from different tissues or from gene-targeted mice with known vascular abnormalities, we demonstrate the ability of AutoTube to determine vascular parameters in close agreement to the manual analyses and to identify statistically significant differences in vascular morphology in tissues and in vascular networks formed in in vitro assays.
Highlights
Blood vessels and lymphatic vessels play important roles in diseases like cancer and inflammation [1,2,3,4]
A manual explaining the installation and step-by-step use of AutoTube can be found in the Electronic Supplementary Material
The image analysis toolbox of AutoTube is available as a graphical user interface (GUI) and has been developed in the MATLAB (The Mathworks, Natick, MA, USA) numerical programming environment
Summary
Blood vessels and lymphatic vessels play important roles in diseases like cancer and inflammation [1,2,3,4]. To investigate and model (lymph)angiogenic processes in vitro, tube formation assays are frequently performed [13]. In these assays, the formation of vessel-like structures (tubes) by endothelial cells in gels containing extracellular matrix components is captured in 2D-microscopic images at a specific time point, followed by an imagebased quantitative analysis of the vascular network (most importantly of tube length) [13, 14]. Palm et al [20] recently developed an efficient framework to simulate and to study the vascular network formation Their model basically captures the self-organisation of endothelial cells into vascular network-like structures by considering cell shape information, cell adherence and their movements. A major factor that has limited their widespread use has been that—with the exception of the study by Palm et al [20]—the source codes of these works are not available and the tools cannot be extended or updated
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