Automated analysis of imaged phenotypes enables fast and reproducible quantification of biologically relevant features. Despite recent developments, recordings of complex networked structures, such as leaf venation patterns, cytoskeletal structures or traffic networks, remain challenging to analyze.
An open source application for the visualization and analysis of 4D biological datasets. Developed by researchers, it is primarily used for the analysis and quantification of 4D live-imaged confocal data. The software's modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.
It is an organized collection of software modules for image data handling, pre-processing, segmentation, inspection and editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks.
Allows automatic reconstruction of entire tissue blocks. AnalyzeSkeleton calculates the optimum transformation at each pyramid level. It is able to store cellular-level phenotypic information. The tool (1) acquires images, (2) automatically and rigidly registers them, (3) segments the structures of interest, (4) groups their resulting contours, (5) locally or elastically refines registration, and (6) reconstructs structure in 3D based on the grouped contours.
Proposes a large collection of generic tools based on mathematical morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins. The library provides different categories of functions, corresponding to standard image processing workflows: (i) image processing and filtering; (ii) segmentation; (iii) post-processing; (iv) quantitative analysis; (v) library re-usability. The cell-resolved data provided by MorphoLibJ will be useful for the analysis of cell lineage, and the modelling of plant growth and morphogenesis in 3D.
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.
Computes a 3D triangular mesh of the tissue. DRACO-STEM is based on the dualization of a simplicial complex of adjacency, and the triangulation and optimization of the resulting polyhedral geometry to proceed. This tool follows three steps for the processing: delaunay complex creation, adjacency complex optimization and dual reconstruction. It was applied to triangular tissue meshes generated from a dataset of segmented tissue images.
A software tool that can be used to analyse confocal images of plant cells. Image analysis algorithms are used to extract the network structure of all cells. This information is then used to perform quantitative analysis on the cell structure, and additional analysis through the use of an extensible plug-in system.