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Biological network reconstruction software tools | Bioimaging

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…
MorphoGraphX
Desktop

MorphoGraphX

An open source application for the visualization and analysis of 4D biological…

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…

MorphoLibJ
Desktop

MorphoLibJ

Proposes a large collection of generic tools based on mathematical morphology…

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…

CellSeT
Desktop

CellSeT

A software tool that can be used to analyse confocal images of plant cells.…

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…

KymoRod
Desktop

KymoRod

Graphical User Interface for studying the growth of plant hypocotyl and root.…

Graphical User Interface for studying the growth of plant hypocotyl and root. KymoRod allows to select a collection of images following the growth of a plant organ. Several processing steps can be…

img2net
Desktop

img2net

A robust approach to reconstruct 2D and 3D (non-)biological spatial networks…

A robust approach to reconstruct 2D and 3D (non-)biological spatial networks from gray-scale image data. By constructing weighted networks and computing their seminal network properties, img2net…

iRoCS Toolbox
Desktop

iRoCS Toolbox

An interactive Qt4 analysis tool for attaching the intrinsic root coordinate…

An interactive Qt4 analysis tool for attaching the intrinsic root coordinate system to 3-D confocal recordings of the Arabidopsis root apical meristem. This allows quantitative comparative studies of…

RootNav
Desktop

RootNav

A software tool for quantification of root system architectures in a range of…

A software tool for quantification of root system architectures in a range of plant species, grown and imaged in a variety of ways. The expectation-maximization algorithm is used to classify the…

NEFI
Desktop

NEFI Network Extraction From Images

A tool that extracts graphs from images of networks originating in various…

A tool that extracts graphs from images of networks originating in various domains. NEFI provides a platform allowing practitioners to easily extract graphs from images by combining basic tools from…

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