Useful Links

Plants


  1. IPPN

    International Plant Phenomics Network. IPPN is an international consortium that will boost plant phenotyping science by developing novel technologies and concepts used for the application of plant production and the analysis of ecosystem performance.

  2. EPPN

    European Plant Phenotyping Network. This project will establish the network that integrates European plant phenotyping efforts and builds a competitive community to the goal of the understanding of the link between genotype and phenotype as well as their interaction with the environment.

  3. DPPN

    German Plant Phenotyping Network. DPPN is a Germany funded project that partners undertake a joint research program and share their phenotyping infrastructure within networking activities.

  4. JPPC

    The Jülich Plant Phenotyping Centre. This project is with aims to elucidate the functional role of gene networks under natural conditions with the aid of the development of non-invasive phenotyping tools and methods as well as the existing genetic resources.

  5. PHEOME

    PHEOME, launched in 2012, is a project funded by French investment for the future. It will provide France with an up-to-date, versatile, high throughput infrastructure and suite of methods allowing characterization of panels of genotypes of different species (important crop species) under scenarios associated with climate changes.

  6. APPF

    The Australian Plant Phenomics Facility. APPF is developed to alleviate the "phenotyping bottleneck" by utilizing high throughput plant phenotyping and "reverse phenomics" approaches with aims to probe and improve plant function and performance.

  7. Phytomorph

    Phytomorph is a project funded by the NSF Plant Genome Research Program. The main premise of the Phytomorph project is that technologies for studying the growth and development of plants must become more quantitative and higher throughput if the most is to be made of current and future genetic/genomic resources. Phytomorph is dedicated to developing technologies to quantify plant development through the application of machine vision, image acquisition, high throughput computing, and data analysis.

  8. 1001 Genomes Project

    A project launched at the beginning of 2008 with a goal to discover the genome-wide genetic variants contributing to adaptation to diverse environments in 1001 strains (accessions) of Arabidopsis. The resulting information has been tested in a GWAS for 107 phenotypes and is ultimately paving the way for a new era of genetics that identifies alleles underpinning phenotypic diversity across the entire genome and the entire species.

  9. Maize HapMap

    The Maize Diversity Project (Panzea, Cornell University). This project aims to decode the genetic architecture underling variation in maize (Zea mays) quantitative traits and to evaluate our ability to predict phenotype from genotype. Based on this project, a comprehensive "phenomic" association analysis has been tested on several key traits involved in leaf development and disease resistance.

  10. Rice HapMap

    The Rice Haplotype Map (HapMap) Project. Several ecologically or agronomically important traits have been tested for genotype-phenotype associations under this project. The project has a long term goal to provide a repertoire of the the genetic variants in rice that facilitate the genetic mapping of complex traits.

Humans


  1. The International HapMap Project

    The International HapMap Project is an organization that aims to develop a haplotype map (HapMap) of the human genome, which will describe the common patterns of human genetic variation. HapMap is a key resource for researchers to find genetic variants affecting health, disease and responses to drugs and environmental factors. The information produced by the project is made freely available to researchers around the world.

  2. The 1000 Genomes Project (TGP)

    The 1000 Genomes Project, launched in January 2008, is an international research effort to establish by far the most complete and detailed catalogue of human genetic variations, which in turn can be used for association studies relating genetic variation to disease.

  3. The Personal Genome Project (PGP)

    PGP is a long term, large cohort study which aims to sequence and publicize the complete genomes and medical records of 100,000 volunteers, in order to enable research into personal genomics and personalized medicine. The project will publish the genotype of the volunteers, along with extensive information about their phenotype: medical records, various measurements, MRI images, etc.

  4. Human Epigenome Project (HEP)

    Human Epigenome Project (HEP) is a international science project, with the stated aim to "identify, catalog, and interpret genome-wide DNA methylation patterns of all human genes in all major tissues"

  5. The Wellcome Trust Case Control Consortium (WTCCC)

    The WTCCC aims were to exploit progress in understanding of patterns of human genome sequence variation along with advances in high-throughput genotyping technologies, and to explore the utility, design and analyses of genome-wide association (GWA) studies.

  6. OnlineMendelian Inheritance inMan (OMIM)

    OMIM is a database that catalogues all the known diseases with a genetic component, and links them to the relevant genes in the human genome and provides references for further research and tools for genomic analysis of a catalogued gene.

  7. The Human Variome Project (HVP)

    The Human Variome Project is the global initiative to collect and curate all human genetic variation affecting human health and with the mission is to improve health outcomes.

  1. LemnaTec

    An robotic greenhouse system that uses non-destructive imaging to monitor plant growth under fully controlled conditions in high-thoughput. The LemnaTec platform aims to visualise and analyse the biology beyond human vision through imaging automatisation.

  2. PHENOPSIS

    An automated platform developed by Optimalog (France) for reproducible phenotyping of plant responses to soil water deficit in Arabidopsis (Arabidopsis thaliana). The PHENOPSIS platform allows to weight, irrigate precisely and take a picture of more than 500 individual plants in rigorously controlled conditions. [Reference]

  3. Phenodyn

    An platform to measures growth rate and transpiration rate every minute, together with environmental conditions (current throughput: 480 plants). [Reference]

  4. GROWSCREEN

    An in-house system used in the Jülich Plant Phenotyping Centre (JPPC) to study leaf growth and fluorescence and root architecture in large plant populations. [Reference]

  5. GROWSCREEN FLUORO

    An in-house system used in JPPC to determine chlorophyll-fluorescence images by PAM light protocoll. [Reference]

  6. GROWSCREEN 3D

    A pioneered solution developed for 3D analysis of leaves in tobacco (Nicotiana tabacum). It enables more accurate measurements of leaf area and extraction of additional volumetric traits.

  7. TraitMill

    A high-thoughput gene engineering system developed by CropDesign that enables large-scale plant transformation and automated high resolution phenotypic evaluation of crop performance in rice (Oryza sativa). [Reference]

  8. RootReader3D

    An imaging and software platform designed for high-throughput 3D analysis of plant roots. RootReader3D was applied to 3D root reconstructions and architecture descriptor quantification during rice seedling development. [Reference]

  9. GlyPh

    GlyPh is a low-cost platform for phenotyping plant growth and water use. The platform allows the evaluation of up to 120 plants growing in individual pots. [Reference]

  10. PlantScan 3D meshes

    A novel automated screening platform and mesh-based technique developed for high-throughput 3D plant analysis. It was initially used for the analysis of aerial-parts in cotton (Gossypium hirsutum) and demonstrated highly accurate when comparing with with manual measurement data. [Reference]

  1. HTPheno

    An open source image analysis pipeline based on ImageJ. It can be used for the analysis different phenotypic measurements such as height, width and projected shoot area of the plants. HTPheno is demonstrated to use in a analysis of high-thoughput phenotyping data of barley (Hordeum vulgare) plants from the LemnaTec system. [Reference]

  2. LAMINA

    A software for the automated analysis of images of leaves for various plant species. It enables rapid quantification of leaf size (area) and shape (blade dimensions) parameters.

  3. HYPOTrace

    HYPOTrace is an image analysis software for measuring hypocotyl growth and shape demonstrated on Arabidopsis seedlings undergoing photomorphogenesis. It is used in the Phytomorph project. [Reference]

  4. PhenoPhyte

    PhenoPhyte is an application that allows plant area to be calculated from photos of Arabidopsis rosettes taken using a defined imaging protocol. Although developed and optimized for use with Arabidopsis rosettes, it can be used with rosettes or detached leaves from other species. [Reference]

  5. Integrated Analysis Platform (IAP)

    IAP is developed as a comprehensive framework for high-throughput phenotyping in plants, which enables us to extract a high-dimensional list of plant traits from real-time images to quantify the plant growth and performance. IAP is anticipated as an open and extensible platform will help collaborate between phenomic and genomic research communities. [Reference]

Root


  1. GiA Roots

    GiA Roots (General Image Analysis of Roots) is a software for the high throughput analysis of plant root system architecture. GiA Roots has been designed to help scientists and breeders quantify the structure of plant root system architecture, regardless of their prior training in mathematics and computer science. [Reference]

  2. WinRHIZO

    An image analysis system specifically designed for root measurement in forms of morphology, topology, architecture, color analyses and so on. WinRHIZO includes both image acquisition components and computer programs to meet different needs and budgets. [Reference]

  3. GROW MAP-root

    GROW Map-toot is an imaging pipeline for the analysis of spatio-temporal dynamics of expansion growth in roots.

  4. RootTrace

    RootTrace is a software tool being developed at CPIB to allow the automatic and high throughput measure of root length, and extra associated measures such as curvature. The user must supply start points for each root, and exemplar patches of nearby background. The software will then trace the main root to the tip, in every image in a timeseries, and record the results. [Reference]

  5. SmartRoot

    SmartRoot is a semi-automated image analysis software which streamlines the quantification of root growth and architecture for complex root systems. The software combines a vectorial representation of root objects with a powerful tracing algorithm which accommodates to a wide range of image source and quality. [Reference]

  6. RootReader2D

    The RootReader software package provides free, publically available image processing and analysis tools for root system images taken from various fixed imaging sources. RootReader2D software was designed to automatically measure root lengths from digital root images. RootReader2D measures, records, and displays root system lengths while also storing processing information in xml-formatted RR2Dat data files. [Reference]

  7. RootReader3D

    RootReader3D software was designed to reconstruct and quantify 3D root system architecture descriptors from 2D rotational image sequences. [Reference]

  8. RootNav

    RootNav is a software tool designed to facilitate the reconstruction and quantification of complex root architectures. Semi-automated reconstruction makes the analysis of many images extremely quick and straightforward. Root data can be exported, and then analysed in bulk using the supplied viewer tool. [Reference]

  9. GROWSCREEN Root

    GROWSCREEN-Root is a image-based software, which allows the automatic analysis of root architecture.

  10. EZ-RHIZO

    EZ-Rhizo software enables the analysis of images of roots grown on two-dimensional media such as agar plates. The software provides a semi-automated system for root detection, measurement of multiple parameters relevant to the root architecture, data storage and data analysis. It is ideally suited for developmental and phenotypic descriptions of individual plants and plant species, accessions, and mutants, and of growth under varying nutritional and environmental conditions. The program facilitates new research perspectives in the areas of functional genomics, breeding and QTL analysis, and in predictive analysis of plant performance. [Reference]

  11. Rootfly

    Rootfly is a free, open-source software application to aid researchers in minirhizotron image analysis. Users can use the software to measure the length, diameter, and color of roots, as well as the birth and death rates. The software is designed to be easy to use, with a minimal number of mouse clicks needed to perform each operation, and with all the data for an experiment stored in a single RFY file. [Reference]

  12. RootView

    RootView was developed for tracing and measuring the growth of roots in minirhizotron images obtained with a video camera.

  13. RooTracker

    RooTracker is a program designed to help researchers collect data from minirhizotron and other root images.

  14. DART

    DART (Data Analysis of Root Tracings) is freeware based on human vision to identify roots, particularly across time-series. [Reference]

  15. IJ_Rhizo

    IJ_Rhizo is an ImageJ macro for the batch processing of scanned images of root samples physically separated from soil by washing. IJ_Rhizo automatically generates root length and radius measurements. [Reference]

  16. RootArray

    RootArray is an imaging pipeline that includes automated tracking of growing roots, automated image acquisition and gene expression quantification. [Reference]

  17. RootScan

    RootScan is an imaging software designed to codify anatomical features of root cross sections from microscope digital images. [Reference]

  18. RooTrak

    RooTrak is an open-source tool, developed to aid in the separation process of plant roots from the surrounding soil, in X-ray micro computed tomography (µCT) images. The tool facilitates the extraction and visualisation of plant root systems and allows the quantification of certain root system traits. [Reference]

  19. RootScape

    RootScape is a landmark-based allometric method for rapid phenotyping of root system architecture (RSA) using Arabidopsis as a case study. [Reference]

Leaf


  1. LeafAnalyser

    An automated image processing solution specifically developed for leaf phenotyping (in Arabidopsis), although it can be extended to use in any 2D image-processing application. [Reference]

  2. WinFOLIA

    WinFOLIA is a computer image analysis system that accurately do morphological measurements on broad leaves. [Reference]

  3. GROW MAP-leaf

    GROW MAP-leaf is a Digital Image Sequence Processing Setup for monitoring of leaf growth via digital image sequence processing.

  4. Rosette Tracker

    Rosette Tracker is a new open source image analysis tool for evaluation of plant shoot phenotypes. This tool is not constraint to one specific monitoring system and can be adapted to different low budget imaging set ups and requires minimal user input.[Reference]

Seed


  1. WinSEEDLE

    WinSEEDLE is an image analysis system specifically designed for needle and seed morphology and disease analysis. [Reference]

  2. SmartGrain

    SmartGrain is a computer program for measuring seed size. This software can measure seed size in images. [Reference]

  3. GERMINATOR

    GERMINATOR is a simple, highly cost-efficient and flexible procedure for high-throughput automatic scoring and evaluation of germination that can be implemented without the use of complex robotics.[Reference]

Cell


  1. WinCELL

    WinCELL is an image analysis system specifically designed for wood cells analysis. It can quantify the changes in wood structure over annual rings. [Reference]

Abiotic stress


  1. ...

    Drought stress [Reference]

Biotic stress


  1. PHENOTIC

    The authors describe an image analysis procedure for quantifying the leaf area impacted by the pathogen. In a perspective of high throughput phenotyping, the procedure was automated with the software R. The interest of this image analysis procedure for assessing the levels of quantitative resistance is illustrated with the quantitation of disease severity on five commercial varieties of bean inoculated with Xff CFBP4834-R. [Reference]

  1. ImageJ

    ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. [Reference]

  2. ImageJ2

    The ImageJDev project is developing version 2.0 of ImageJ, referred to as "ImageJ2" or "IJ2" for short. It is a complete rewrite of ImageJ, but includes ImageJ1 with a compatibility layer, so that old-style plugins and macros can run the same as in IJ1.

  3. Fiji

    Fiji (Fiji Is Just ImageJ) is an Open Source image processing package based on ImageJ. Fiji's main purpose is to provide a distribution of ImageJ with many bundled plugins. Fiji features an integrated updating system and aims to provide users with a coherent menu structure, extensive documentation in the form of detailed algorithm descriptions and tutorials, and the ability to avoid the need to install multiple components from different sources. [Reference]

  4. μManager

    μManager is a software package for control of automated microscopes. Together with the image processing application ImageJ, μManager provides a comprehensive, freely available, imaging solution.

  5. Icy

    Icy is an open community platform for bioimage informatics. Icy provides the software resources to visualize, annotate and quantify bioimaging data. [Reference]

  6. BioImageXD

    BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images. BioImageXD is written in Python and C++, using wxPython for the GUI, and leverages the power of the Visualization Toolkit (VTK) for multi-dimensional image processing and 3D rendering. BioImageXD also uses the Insight Segmentation and Registration Toolkit (ITK) for segmentation and other image processing tasks. [Reference]

  7. CellProfiler

    CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. [Reference]

  1. Plant Image Analysis

    This website lists a lot tools about image analysis.

  2. JIBtools (Journal of Integrative Bioinformatics - Tool Lists)

    JIBtools provide a new approach to sum up a number of different tools associated with categories applying to Integrative Bioinformatics.

Acknowledgement
  • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

  • The Federal Office of Agriculture and Food

The Federal Office of Agriculture and Food

  • The Robert Bosch Stiftung

The Robert Bosch Stiftung

  • The National Natural Science Foundation of China

The National Natural Science Foundation of China

  • Zhejiang University

Zhejiang University