Fully automated Root Image Analysis - faRIA v0.1

Introduction

faRIA tool was developed to enable quantitative anaysis of plant root growing in a opaque soil environmnet or artificial substrates (e.g., Agar gels) in a fully automated manner using pretrained deep learning models.

Key Features

The faRIA tool performs fully automated segmentation root structures of all images stored in a target folder or one single image at a time per user click. Subsequently, segmented root structures of each single image are quantitatively characterized in terms of various traits including area, length, width, volume, etc..

Downloads

download Windows x64 (200MB)
download Linux (200MB)

By downloading, installing and/or using this software the user agrees with the following license conditions.

This software requires MATLAB run time libraries (2021a) to be installed:

MATLAB run time for Windows x64 (~2GB).
MATLAB run time for Linux (~2GB).

Some information on dependencies of the MATLAB run-time components in Linux can be found here: https://de.mathworks.com/matlabcentral/answers/358052-is-there-a-list-of-matlab-runtime-dependencies.

General hardware requirements for MATLAB applications can be found here: https://de.mathworks.com/support/requirements/matlab-system-requirements.html.
For processing of image files of the 4-8 MP size such as provided with the supplementary data, 8GB or more RAM is recommended.

Quick Start

For install notes and further informations, please see the Quick Guide.

References

[1] Narisetti N, Henke M, Seiler C, Junker A, Ostermann J, Altmann T, Gladilin E. Fully-automated root image analysis (faRIA). Sci. Rep. 11 (2021) 16047. https://dx.doi.org/10.1038/s41598-021-95480-y

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