Quantitative magnetic resonance imaging of Scots pine seeds and the assessment of germination potential

This dataset contains all the raw source data and MATLAB analysis functions that comprise the study:

Quantitative magnetic resonance imaging of Scots pine seeds and the assessment of germination potential

Canadian Journal of Forest Research | DOI: 10.1139/cjfr-2021-0273.

Tuomainen, TV (1), Himanen, K (2), Helenius, P (2), Kettunen, MI (3), Nissi, MJ (1,4)*
1. University of Eastern Finland, Department of Applied Physics, Kuopio, Finland
2. Natural Resources Institute Finland, Suonenjoki Unit, Suonenjoki, Finland.
3. University of Eastern Finland, Kuopio Biomedical Imaging Unit, A.I. Virtanen Institute for Molecular Sciences, Kuopio, Finland 
4. University of Oulu, Research Unit of Medical Imaging, Physics and Technology, Oulu, Finland

*Corresponding author:
Mikko J. Nissi
Department of Applied Physics,
University of Eastern Finland
POB 1627
FI-70211, Kuopio, Finland
[e-mail]
[phone]

Keywords: Pinus sylvestris, seed germination, MRI, radiography, relaxation time mapping

Study and data description

Altogether 90 Scots pine (Pinus sylvestris L.) seeds were MR imaged using RAREVTR, MSME, MGE and ZTE pulse sequences with reference radiograph from each seed.

The data includes MR images and relaxation time data as well as individual X ray radiographs of Scots pine seeds. 

The data includes all data ('fid' and '2dseq' for MRI, and .jpeg/.png for radiographs), metadata (acquisition and reconstruction MRI parameters), figures of manuscript, and calculated relaxation time maps (in MATLAB MAT-file format).

Included folders and files in the zenodo_repo_scotspine_MRI_zip_20012022 are:

additional_info_scotspine: Information on the seed batches, their germination and structure in .xlsx file format. Translated into English from Finnish on 06.10.2021.

manuscript_figures: Figures in .eps vector file format (fig1.eps-fig7.eps)

matlab_scripts: Contains MATLAB functions and scripts for data analysis of the MRI data, processed together with 'aedes' GUI (aedes.uef.fi/, redirects to github.com).

mri_scotspine: Contains the MRI data using 5 mm and 10 mm RF coils at 11.7 T (Bruker). The folders 'discard_folder/' contain ZTE data that are not processed with carbon_collector.m MATLAB script (i.e. processed separately).

radiography_scotspine: Contains radiographs of invidual seeds in two folders: old (lower resolution, Faxitron MX-20, Faxitron Bioptics LLC, Tucson, Az, USA) and new (higher resolution, Faxitron MultiFocus, Faxitron Bioptics LLC, Tucson, Az, USA).

readme.txt: More information on the file and folder structure and datatypes.

Please see the included readme.txt for further details.

(Teemu Tuomainen, Jan 25, 2022)