Germination Detection Assistance Tool - gdat v0.1

Introduction

gdat was developed as assistance tool aiming to provide computer aided support during the detection of time point of germination (to be precise: the time point of first occurrence of the shoot at the surface). The tool is designed to process a set of fluorescence images in a fully automated way [1].

The detection of germination and the first occurrence of the shoot is an important information for many biological questions. To detect the first occurrence of shoots one can make use of the fact that chlorophyll containing plant organs are fluorescing red. Therefore, the occurrence of such red pixels within an image can be taken as indicator for germination/occurrence of a shoot.

After a very short calibration, the tool automatically counts the number of red dots within a defined radius around the expected plant location. The number of red dots is further used to determine if plant material is visible or not.

Key Features

The gdat is implemented to automatically process a set of fluorescence images consisting ether of one, six or 12 plants in order to calculate the number of red pixels within each spot. The results are written into a database file.

Downloads

download Windows x64 (256MB)
download Linux (291MB)
download sample images (122MB)
Quick Guide (12MB)

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

This software requires MATLAB run time libraries (2018a) to be installed:

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

Windows users should also install the run-time components from the following link: https://www.microsoft.com/en-us/download/details.aspx?id=48145.

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] Henke, M., Junker, A., Altmann, T., Gladilin, E. Germination detection and quantification assistance tool, (unpublihsed)

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