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.
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.
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.
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.
Offers a platform for handling dendritic structures. TREES Toolbox is a standalone software that allows users to create realistic synthetic branched structures and to automatically rebuild neuronal branching. The application provides methods to investigate and visualize both dendritic and axonal trees as well as their branching. The application is also able to compare multiple branching structures.
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.
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