Quantitative magnetic resonance imaging of Scots pine seeds and the assessment of germination potential
Bibliographic record
Abstract
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 mikko.nissi@uef.fi +358-50-5955517 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)
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.005 | 0.004 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".