Oxygen Imaging Respiration Tool - oxIR v0.1

Introduction

oxIR was developed by the Image Analysis group of IPK Gatersleben within the scope of cooperation with R. Zornow [1,2] aiming to provide an efficient possibility to estimate oxygen content and so respiration rates of seed samples of grid cells over time obtained by abc facility. The abc facility generates fluorescence images as time series of a defined grid.

Key Features

The oxIR tool is implemented to semi-automatically process a time series of abc images (a set of images) consisting of an arbitrary number of samples in order to estimate the oxygen content for each time point and further to calculate the rate of change during time, i.e. the respiration rate of seed samples.

Downloads

download Windows x64 (247MB)
download Linux (283MB)
download sample data (100 images) (136MB)
download sample data (200 images) (273MB)
Quick Guide (3MB)

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

This software requires MATLAB run time libraries (2018b) 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] Zornow, R. M.S. thesis, (unpublihsed)
[2] Henke, M. Zornow, R., Rolletschek, H., Gladilin, E. Automated processing of sensor array images for estimation of oxygen content, (unpublihsed)

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