Kinematics analysis software tools | Macroscopy and basic digital camera imaging
A major challenge in plant biology is to understand organ growth in terms of underlying molecular processes. All known hormones, nutrition and many environmental factors influence organ growth. Despite major advances in our understanding of the underlying signaling networks, little is known on how these networks are connected to observed changes in organ growth. Advances in this area require efficient kinematic analysis methods that bridge the gap between molecular and organ scale by providing information at the cellular and supra-cellular scale. In recent years many tools have been developed to measure the kinematics of growing organs.
Analyses seed germination growing in a high-throughput and automatic way. Germinator employs the information from two different color threshold studies on a single picture, which circumvents alignment problems. It can examine the relevant parameters from the germination-time curve. This tool enables analysis of any type of cumulative germination data and is not restricted to any plant species.
Allows users to streamline the quantitative analysis of root growth and architecture of complex root systems. SmartRoot is able to capture, store, present, and process data that are linked to location. This tool uses several algorithms designed for root tracing and has been validated on a range of image spatial resolution, noise, and contrast.
Allows acquisition and evaluation of high-quality images of plants that had been raised in standard laboratory conditions. GROWSCREEN incorporates standard procedures of single-image processing with an automated setup. It allows recognition of light-induced growth acclimation responses within 24 h. This tool can be useful for ecophysiology studies and to analyse effects of agrochemicals or xenobiotica as well as differences between plant lines caused by their varying genetic backgrounds.
Monitors the growth of the plant roots as well as the activity of genes that respond to environmental stress. GLO-Roots can be used to measure the water content of soil at different depths and how this influences the architecture of the root. It provides functions permitting different type of analyses on images for instance detecting the position, length, and direction of roots, as well as their shape and depth.
A high-throughput, automatic method to trace Arabidopsis (Arabidopsis thaliana) seedling roots grown on agarose plates. RootTrace combines a particle-filtering algorithm with a graph-based method to trace the center line of a root. This top-down approach is robust to a variety of noise effects and is reasonably flexible across different image sets. The resulting tool requires minimal interaction from the user and is able to process long time-lapse sequences with user interaction only required on the first frame.
An image-analysis program developed to study spatio-temporal patterns of growth and curvature of roots. KineRoot tracks the displacement of patterns created by the graphite particles over space and time using three search algorithms. KineRoot is capable of analyzing a large number of images to generate local root growth and root curvature data over several hours, permitting kinematic analysis of growth and gravitropic responses for a variety of root types.
Allows measurement of scanned images of washed root samples, written as a macro for ImageJ. IJ_Rhizo is a program that automates a series of ImageJ commands. The software allows researchers to compute root length measurements. It automatically generates root radius distributions for each sample analyzed. Some options are included for customizing: image resolution; the size of image border to be excluded from processing; background particle cleaning; root length correction; and the choice of automatic versus user-defined thresholding.