Regensburg 2016 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 48: Posters - Bioimaging and Spectroscopy

BP 48.1: Poster

Mittwoch, 9. März 2016, 17:00–19:00, Poster C

NET- the Network Extraction Tool — •Jana Lasser — MPI for Dynamics and Self-Organization, Göttingen, Germany

We present the Network Extraction Tool (NET). The tool is especially designed for high-throughput semi-automated analysis of biological datasets containing networks of very large sizes. Applied to a network, NET extracts information about its geometry (node positions and edge radii) as well as information about the topology (neighbourhood relations). The information NET collects provides a basis for quantitative research of the networks in question. The framework starts with the segmentation of the image and then proceeds to vectorization using methodologies from optical character recognition. After a series of steps to clean and improve the quality of the extracted data the framework produces a graph in which the network is represented only by its nodes and edges. The networks extracted by NET are comparable to manually extracted networks with regards to their quality but take significantly less time to generate. Additionally, the extracted networks are very easy to handle computationally. Several projects researching biological networks such as leaf veins, insect trachea and blood vessels already use NET for their data acquisition. As it is an open source tool based on a collection of python scripts feel free to find and try out the software at https://github.com/JanaLasser/network_extraction.