DOI: 10.5281/zenodo.13856316
title: Arabidopsis Inflorescence Images from MAGIC Density Experiments - 3

description: This dataset contains images of mature inflorescences, collected from the second batch of the three experiments conducted on the Multiparent Advanced Generation Inter-Cross (MAGIC) population for Arabidopsis. The dataset has been used for phenotypic and genetic analysis in plant research, as well as for the development of AI pipelines for Arabidopsis fruit phenotyping.

The images are organised into two parts according to the treatments: "group" or "isolation". 

The full collection of images from all three batches are:

AT023: 10.5281/zenodo.13853394

AT024: 10.5281/zenodo.13856248

AT025: 10.5281/zenodo.13856317
description: The images were acquired from experiments conducted at the National Plant Phenomics Centre (NPPC), Aberystwyth University, United Kingdom. 

## Experiments

The original experiments aimed to investigate the relationship between genetic variation and plant traits under two different treatments:- Grown in isolation- Grown in groups (4 plants of the same Recombinant Inbred Line (RIL))

The detailed design of the experimentation is outlined by Biernaskie, Gina A. Garzon-Martinez et al. in [1], but key points include:- Three experiment batches were carried out. - For each experimental batch, three replicates were conducted for each sample, i.e. a MAGIC RIL + treatment combination.- Replicates were block randomised, with each replicate randomised as a separate block to ensure diversity and avoid bias.

The Arabidopsis MAGIC population used in these experiments was as described in [2]

### Growing ConditionsPlants were grown in 6 cm diameter pots, which were half-filled with vermiculite (to restrict plant growth) and topped with a 30% grit/sand and 70% Levington F1 peat-based compost mixture.All plants were grown on an automated watering platform at the NPPC. Pots were filled to a uniform weight to maintain consistency across experiments.Daily irrigation was provided, ensuring a 75% gravimetric water content by automatically weighing and watering each plant from above.

## Image Acquision

For each plant, the mature inflorescence or stem, along with attached fruits, was harvested and scanned using a flatbed scanner (Plustek OpticPro A320) at a resolution of 300 dpi. The images were saved in PNG format with a resolution of 3600x5100 pixels.

### File naming convention

Each image corresponds to one individual plant, and the file names follow a consistent naming convention to encode information about the experiment and the specific plant. The naming format is:ATddd_wwwxyz_ppp.png

Breakdown of the File Naming Convention:ATddd: This represents the Experiment ID or Batch ID (e.g., AT025).www: Refers to the MAGIC CODE, which is the Recombinant Inbred Line (RIL) number (e.g., 471).x: This indicates the imaging modality, which is always "3" for all samples in this dataset.y: Refers to the treatment type:1 = Plant grown in isolation.4 = Plant grown in a group of 4.z: Denotes the replicate number for the specific RIL and treatment (ranging from 1 to 3).ppp: Represents the plant number within the same pot (group), ranging from 001 to 004.

Example 1: AT025_471341 002.pngAT025: Experiment batch ID 025.471: MAGIC RIL number 471.3: Imaging modality (same for all samples).4: Treatment type (grown in a group).1: Replicate number 1.002: The second plant in the pot (group).

Example 2: AT024_169312 001.pngAT024: Experiment or batch ID169: Magic RIL number 1691: Treatment id 1 - grown in isolation2: RIL+treatment replicate ID001: The specific plant number within the same pot

 

## References[1] Jay M. Biernaskie, Gina A. Garzon-Martinez, Fiona M.K. Corke, and John H. Doonan. Uncovering the hidden genetic basis of plant competitiveness and group productivity, under revision, 2024.[2] Paula X. Kover et al. A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana, PLOS Genetics, 5(7), 2009.  https://doi.org/10.1371/journal.pgen.1000551