Arabidopsis Inflorescence Images from MAGIC Density Experiments - 3

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 Conditions
Plants 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.png
AT025: 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.png
AT024: Experiment or batch ID
169: Magic RIL number 169
1: Treatment id 1 - grown in isolation
2: RIL+treatment replicate ID
001: 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