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Allows analysis of images of roots grown on 2D media such as agar plates. EZ-Rhizo is a semi-automated application developed for measuring multiple root system architecture (RSA) parameters of young plants grown in vertical Petri dishes. The software combines non-invasive image acquisition, measurement of multiple RSA parameters, data storage and data analysis. It is suitable for the phenotypic description of individual plant species, accessions and mutants grown under varying nutritional and environmental conditions.
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.
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 automated tool for making high-resolution measurements of Arabidopsis hypocotyls may find many uses in plant biology research and education. HYPOTrace is able to measure light-induced hypocotyl inhibition, apical hook opening, phototropism, and nutation with a high degree of automation and resolution. HYPOTrace is expected to benefit seedling development research, particularly in the photomorphogenesis field, by replacing many tedious, error-prone manual measurements with a precise, largely automated computational tool.
ARTT / Analyser for root tip tracks
An image-analysis tool to study the kinematics of the root tip (apex). ARTT implementation combines a segmentation algorithm with additional software imaging filters in order to realize a 2D tip detection. The resulting paths, or tracks, arise from the sampled tip positions through the acquired images during the growth. ARTT allows work with no markers and deals autonomously with new emerging root tips, as well as handling a massive number of data relying on minimum user interaction. Consequently, ARTT can be used for a wide range of applications and for the study of kinematics in different plant species. In particular, the study of the root growth and behaviour could lead to the definition of novel principles for the penetration and/or control paradigms for soil exploration and monitoring tasks. The software capabilities were demonstrated by experimental trials performed with Zea mays and Oryza sativa.
An image-analysis program for the kinematic study of root elongation. GrowthTracer employs a multiresolution image matching method with a nonlinear filter called the critical point filter (CPF), which extracts critical points from images at each resolution and can determine precise matching points by analysis of only two intact images, without pre-marking by graphite particles. This program calculates the displacement of each matching point and determines the displacement velocity profile along the medial axis of the root. We show a successful application of this novel program for the kinematic analysis of root growth in Arabidopsis thaliana.
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.
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