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A software tool for quantification of root system architectures in a range of plant species, grown and imaged in a variety of ways. The expectation-maximization algorithm is used to classify the initial image, and produce a probability map of regions likely to contain root material. An intuitive user interface allows the user to guide in the detection of complex root paths, including the ability to overcome areas of challenging root structure, or image noise. Measurements can be exported directly, or saved in a database, where additional traits can be calculated later using a simple plug-in system.
LEAF GUI / Leaf Extraction and Analysis Framework Graphical User Interface
Allows analysis the macroscopic structure of veins in leaves. LEAF GUI is a program built upon a series of algorithms designed to threshold, clean, and segment images of leaves in which the vein structure is visible. The software enables users to extract descriptive statistics on the dimensions and positions of leaf veins and the areoles they surround by following a series of thresholding, cleaning, and segmentation algorithms given images of leaves where veins have been enhanced relative to the background.
NEFI / Network Extraction From Images
A tool that extracts graphs from images of networks originating in various domains. NEFI provides a platform allowing practitioners to easily extract graphs from images by combining basic tools from image processing, computer vision and graph theory. Thus, NEFI constitutes an alternative to tedious manual graph extraction and special purpose tools. We anticipate NEFI to enable time-efficient collection of large datasets. The analysis of these novel datasets may open up the possibility to gain new insights into the structure and function of various networks.
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