Permits users to quantify and visually reconstruct averaged root system architectures (RSA) for investigating environment-genotype interactions. EZ-Root-VIS provides a procedure to capture RSA features of many individual plants and to visualize averaged RSAs for different genotypes under various environments or at different time points. The software is useful for studying root growth dynamics, quantitative genetics, and genotype environment interactions.
Serves for effective segmentation of multidimensional datasets. MIB can recognize several number of imaging formats and offers a variety of image processing tools. It also simplifies utilization and quantification of acquired data. It permits users to segment large datasets, to realize 3D visualization, and to quantify images and models. Its parameters enable users to insert plugin s to customize the program for specific needs.
Allows semi-automatic phenotyping of growing seedlings from time-lapse images. HypoPhen was developed to accelerate and standardize hypocotyl-bending measurements. The software can measure the length and orientation of hypocotyls at the given time points. It performs computation and recording of the elongation and bending of the seedlings. HypoPhen can be adapted, by researchers, to their specific need.
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.
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.
Allows users to describe and compare leaf shapes perimeters. LEAFPROCESSOR process bending energy analysis to quantifies the changes in leaf parameter deformation. The principal functions of this software are: (1) organization of the image data, (2) segmentation of leaves in an image, (3) assignment of shape attributes, (4) cluster analysis, (5) classification and (6) creation of regression models.
Allows users to analyze root images using machine learning techniques. PRIMAL trains the Random Forest (RF) model and analyzes data. The software can be used to extract descriptors from large libraries of root images. It was used to predict architectural traits based on automatically-extracted image descriptors and trained on a subset of the whole dataset that had been previously analyzed using a semi-automated tool.
Allows quantitative analysis of high-throughput plant phenotyping data. IAP handles different image sources and assists in organizing phenotypic data by retaining the metadata from the input in the result data set. It provides approaches for data management, image analysis, and result handling for large-scale experiments. IAP includes image-analysis pipelines to examine various traits for other species, such as Arabidopsis, wheat, and barley, and can be adapted to process imaging data from different monitoring systems and camera types.
Provides to researchers mathematical descriptors and output that facilitate the analysis of fruit morphology. Tomato Analyser measures fruit shape attributes with a high-throughput manner and with traits that are difficult to quantify manually. The software is appropriate to evaluate fruit shape quantitative trait loci (QTL) in tomato but can be applied to other fruits and plant organs like seed and leaves.
Allows users to perform automated image analysis of plant roots. RootGraph is a method that employs a weighted graph-based optimization step to produce an automated, primary root identification procedure. It is able to estimate the number, length, and diameter of roots and can separate primary roots from lateral roots. This tool can quantify traits for each primary root as well as each primary root’s associated lateral roots, but can do so under high-throughput conditions.
Allows high-throughput image analysis for plant biologists. Image Harvest is an open-source and flexible framework for processing and analyzing plant images, such as conventional color and fluorescence images. The software allows the simplification of the collection of metadata from the organizational structure of raw image databases. It provides an option for implementing basic statistical functions, as well as several definitions of digital traits to describe plant growth, morphology, and physiological responses.
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.
Provides assistance for calculating contact angles and surface tensions. Drop Shape Analysis is based on a first order perturbation solution of the Young-Laplace equation for axisymmetric sessile drops. This software estimates contact angles via the guidance provided by the global drop contour. It implements (1) DropSnake for shaping the drop and (2) LBADSA, based on the fitting of the Young-Laplace equation to the image data.
Enables growers to take photos of a possibly affected plant with their mobile device. X-FIDO offers a way to upload an image from a mobile device or computer or have an image processed remotely through the cloud by a deep learning system. It is able to send a prompt diagnosis of the specimen detected. This tool discovers low-level features from raw data to automatically detect veins and colors that lead to symptomatic leaves.
Allows controlled experiments to be conducted on soil without compromising factors such as exposure of roots to white light. measuRoots is an R package that presents an efficient pipeline for root growth measurement under water stress allowing an experiment to be set up in an hour and measurements collected quickly at each timepoint via photography. It includes a graphical interface to automate all post processing and analysis steps from the data output of SmartRoot.
Calculates the number and the size of seeds thank to a white paper sheet of standard size as a background. SeedCounter automates evaluation of phenotypic parameters of grains using mobile devices running the Android operational system. It is efficient and sufficiently accurate for the large-scale analysis of phenotypic characteristics in wheat grains. The tool converts pixels into the metric scale to estimate the output values.
Processes high quality leaf images. LeafletAnalyzer generates size and shape parameters for both blades and serrations. It can automatically detect and remove trichomes from leaf images. The tool uses all points (pixels) on leaflet borders for measurements and calculation of leaflet size, shape and serration parameters. Based on Elliptic Fourier transformation, it can generate spectral frequency components for each leaflet.
Enables automated or semi-automated analysis of leaf morphological traits. LAMINA is a program for the quantification of leaf serration, that is used to identify leaf objects and to calculate properties of those objects. The software can aid the screening of large-scale collections of genotypes for forward or reverse genetics as well as equally serving plant breeders. It is suitable for using in a diverse range of species.
Serves for the high-throughput analysis of root system architecture. GiA Roots estimates root system architecture (RSA) traits from a large number of root system images and identify roots from the background, i.e., segmenting the image. It includes: an optional userassisted processing of images, scale calibration, trait selection, image segmentation, and trait measurement.
Measures selected two-dimensional traits from plant images. PhenoPhyte can (1) process images sequences, track objects across images, report temporally varying traits such as growth and herbivory; (2) process choice assay experiments and (3) automatically adjust for variations in scale and lighting. This software is compatible with images of individual leaves and rosettes and allows multiple objects in one frame.
Allows image capture and analysis for measurement of cereal grain size and colour. GrainScan uses utilizes reflected light to capture colour information described in a device independent colour space (CIELAB), allowing comparison of colour data between scanning devices. The software enables the standardized study of grain size, shape and colour. It can be can be implemented for many different plant species that also have regular, approximately elliptical morphology.
Allows the study of standard circumnutation parameters in relation to the geographical direction applicable in various plant species. CT employs Basic Linear Algebra Subroutine (BLAS) for run calculations. It permits users to analyse every single circumnutation in an objective north-south - east-west (NS-EW) plane, which is an advantage over Fourier and autocorrelation analysis as these provide information about frequency only.
Discovers the colony area percentage and an intensity weighted colony area percentage from flatbed scanner acquired images of colony formation assays conducted in multi-well plates. ColonyArea precisely quantifies scanned images of colony formation assays. It employs information about the plate type and the number of selected wells to build a mask that will set the intensity of the pixels belonging to the space in between wells to zero.
Provides automated analysis of nematode size and shape. WormSizer is an open source software written as a plugin for ImageJ/Fiji. This application is designed to work with a standard stereomicroscope or any other source of brightfield images. It can detect multiple worms per image and it returns measurements of length, average width, width at the middle of the nematode, and volume in absolute units. It can also be extended and incorporated into existing tools.
Calculates worm body size from a single image that can potentially contain multiple worms. WormLength features batch analysis of multiple well or plate images. Users can conduct manual inspection to review results of image analysis and adjust errors made in the fully automated analysis. This software removes false positive detection by establishing the size, length and fatness of detected objects. This module is part of the QuantWorm software.
Analyzes C. elegans lifespan, locomotion, body size, and egg laying assay phenotypes. QuantWorm contains several components for image acquisition and image analysis that provides multiple measurements on C. elegans. This software can be easily modified by developers to adapt methods from several popular systems. It can be used with a microscope equipped with a digital camera and motorized stage.
Calculates the stained areas in a Masson Trichrome stained slide as well as the adipose tissue area. FibroQuant is a method for systematic high resolution digital quantification of different tissue types in the heart. This method of fibrosis quantification can be used for several applications like the determination of the fibrosis pattern in the heart could provide an important link for genotype-phenotype relationships in genetic cardiomyopathies.
Reconstructs and analyzes the growth of a plant root system from a time-series of 3D voxelized shapes. DynamicRoots is designed to automatically process a time-series of 3D reconstructions of a growing root system. The software enables high-throughput analysis of local growth response to a wide-range of biotic and abiotic plant-environment interactions.
A software package for automatic phenotyping in C. elegans included in QuantWorm. WormGender is designed for accurate quantification of sex ratio in Caenorhabditis elegans. The software functions include, i) automatic recognition and counting of adult hermaphrodites and males, ii) a manual inspection feature that enables manual correction of errors, and iii) flexibility to use new training images to optimize the software for different imaging conditions. We evaluated the performance of our software by comparing manual and automated assessment of sex ratio. Our data showed that the WormGender software provided overall accurate sex ratio measurements.
Serves for collecting distance and count measurements from images. webpic is a web application that enables images to be measured and processed through an auto-advancing, streamlined workflow. It implements common web languages and productivity apps to streamline the process of collecting distance and count measurements from images and simplifies data collection in research tasks.
Assists users to analyze large-scale image data. This program offers several functionalities such as: acquisition of plant images, transformation of amounts of real-time image data to numerical data, and presentation of these data as graphs. This system can be used by plant biologists and data are automatically acquired and processed. Moreover, this software enables tracking of plant growth.
Allows high-throughput plant phenotyping. HTPheno is an image analysis pipeline that has been developed in a modular way to allow the analysis of images from different phenotyping sources. The software can be useful for measuring phenotypic parameter, such as projected shoot area in top and side view of plants to distinguish different phenotypes.
Estimates leaf area from digital images. Easy-Leaf-Area uses a combination of thresholding, color ratios, and connected component analysis to measure leaf area in individual images in seconds or batch process hundreds of images in minutes. The software separates leaf pixels from various backgrounds and can thus be used for leaf area and crop canopy measurement without masking soil or relying on infrared images to distinguish leaf area from background soil.
Detects diseased from healthy plant tissues and measures percentage of disease severity. Leaf Doctor is a semi-automatic assessment tool for disease severity of individual leaves or other sampling units. It exploits lesion types, leaf shapes, and disease intensities. This mobile application can be used for a general pixel-analysis of spatial patterns for diseases plant tissues, or in fields, forests, or landscapes.
Serves as a convolutional neural network (CNN) model that automatically learns representation for plant categories. Deep-Plant also detects and diagnoses the feature representation learnt by the CNN model via a visualization strategy built on the deconvolutional networks (DN). This method allows to avoid the use of the CNN model as a black box solution.
Calculates the total leaf area and the area with any visible symptom on the leaf. CompuEye splits the leaf image into small squares and assess the average colour of every square. It furnishes option to adjust the area of the square units between 0.1 and 1.0 mm². This tool is able to discover various types of symptoms, based on lack of green colour, and then classifies them into four different categories.
Allows users to measure foliar damage caused by insect herbivory. BioLeaf aims to calculate the intensity of foliar loss in relation to the total leaf area. This method consists of four steps based on techniques of image processing and computational geometry applied to each leaf image: (1) image thresholding, (2) noise removal, (3) border reconstruction using quadratic Bezier curves, and (4) insect herbivory quantification.
Measures in a semi-automatically way the length of the primary root of Arabidopsis seedlings. MyROOT automatically identifies the scale of the image and recognizes the hypocotyls and root tips from young seedlings growing in agar plates to evaluate the root length of each individual plant. It only needs one image of the plate for the analysis and is able to recognize hypocotyls of different ages and morphologies.
Allows automatic classification of ant species using images. FormicID is an image-based ant classification method that consists of an alternative approach to taxonomic identification of ants, based on computer vision and deep learning. The software utilizes a convolutional neural network (CNN) to classify ants at species level. It uses images from AntWeb, an online open database for ecological, taxonomic, and natural history information on ants.
Allows users to measure nematode chemotaxis behavior and features in a browser. NemaCount is available as a Google Chrome Extension and offers a suite of functions that aim to measure and analyze diverse nematode behaviors including chemotaxis, odortaxis, avoidance, and thermotaxis assays. The purpose of this tool is to provide a method for analyzing nematode behavior that could especially be used by researchers to Caenorhabditis elegans research.
Allows estimation of leaf area from scanned images. Black Spot aims to process large multi-species datasets of leaf images. It allows for batch-processing datasets which contain images of leaves across multiple species to produce highly accurate estimates of leaf areas. It serves to standardize data quality when data are collected by large teams or comparisons are made across datasets and regions.
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.
Analyzes root system traits from RGB (red, green, blue) pictures. REST exploits a high-throughput phenotyping method for mature maize root system in the field. This software identifies observing differences between genotypes and nitrogen levels of root system architecture traits (RSAT) at the periphery and interiors of the crowns.
Aims to analyse canopy images. Canopy Analysis can determine the percentage of canopy closure. It reads in the images in a directory, extracts the blue RGB component, and thresholds each image. This tool employs an algorithm based on edge detection to proceed. It can be useful for threshold skyward-looking canopy images and is able to differentiate within- and between-crown gaps with morphological operations.
Enables analysis of lamina images. Lamina2Shape is an image processing algorithm that allows precise measurement of lamina area and an explicit approximation of lamina shape by w(l). The software can be applied on laminae of several species, they can be unrolled on a plane, have an axial symmetry and a lmax: wmax higher than 10. It was used to quantify dimensions and shape of cereal laminae.
Recognizes leaf area, growth and chlorophyll fluorescence. GROW MAP-leaf fixes a leaf in a plane parallel to camera to capture images. It employs near infrared-diodes to illuminate leaf. This tool can calculate divergence to construct growth maps. This tool permits users to conduct optical flow analysis of image sequence resulting in velocity vector fields.
Marks and links results in a non-destructive way. ObjectJ uses vector objects to display points and paths that non-destructively mark images via a transparent layer. This ImageJ plugin stores the graphical objects into a separate project file. A back-and-forth navigation between results and images is available and the results table can incorporate statistics, sorting, color coding, qualifying and macro access.
Analyzes and measures digital images. Bersoft Image Measurement executes automatically measurements or area, radius and length. It uses vectorial layers to draw the different measurements available. Spatial calibration is provided, and can process Elisa and Western Blot arrays. This tool is compatible with several popular image formats.
Computes percentage cover using a photo of the canopy. HabitApp is a tool able to convert pixels to black and white. It includes cut-off value which determines if pixel becomes black or white, enabling users to apply same parameters to all images in the same conditions. This tool is available as a desktop or smartphone application thanks to an Android app.