DOI: 10.5061/dryad.34tmpg4n6
title: Data from: The shape of aroma: Measuring and modeling citrus oil gland distribution

description: From preventing scurvy to being part of religious rituals, citrus are
 intrinsically connected to human health and perception. From tiny
 mandarins to head-sized pummelos, citrus capability of hybridization
 provides a vastly diverse array of fruit sizes and shapes, which in turn
 corresponds to a diversity of flavors and aromas. These sensory qualities
 are tightly linked to oil glands in the citrus skin. The oil glands are
 also key to understanding fruit development, and the essential oils
 contained by them are fundamental in the food and perfume industries. We
 study the shape of citrus based on 3D X-ray CT scan reconstruction of 163
 different citrus samples comprising 58 different species and cultivars,
 including samples of all fundamental citrus species. First, using the
 power of X-rays and image processing, we are able to compare and contrast
 size ratios between different tissues, such as the size of the skin
 compared to the rind or the flesh. Second, we model the fruit shape as an
 ellipsoidal surface, and later we study and infer possible oil gland
 distributions on this surface using principles of directional statistics.
 We finally compare and contrast these overall fruit shape models along
 their gland distributions across different citrus species. This
 morphological modeling will allow us later to link genotype with
 phenotype, furthering our insight on how the physical shape is genetically
 specified in DNA.
description: We selected 51 different citrus varieties with diverse
 morphologies and geographical origins for our analysis. 166 different
 individuals in total were sent for scanning at Michigan State University
 in December 2018 (details of the scanned varities attached) These 166
 samples were arranged into 63 raw scans, one scan per citrus variety
 containing all the replicates. An exception were pummelos and citrons,
 where each sample was individually scanned due to the fruit size. The
 scans were produced using the North Star Imaging X3000 system and the
 included efX software, with 720 projections per scan, at 3 frames per
 second and with 3 frames averaged per projection. The data was obtained in
 continuous mode. The X‐ray source was set to a voltage ranging from 70 kV
 to 90 kV, current of 70 µA, and focal spot size of 7.5 microns. The 3D
 reconstruction of the citrus was computed with the efX-CT software,
 obtaining a final voxel size ranging from 18.6 to 110.1microns for
 different scans (resolution detailed is attached)<br><br>The
 air and debris were thresholded out of each raw scan, and individual
 replicates segmented into separate images. These images were further
 segmented into individual tissues based on their density and location
 within the fruit. For each fruit we thus obtained 3D voxel-based
 reconstructions of their central column, endocarp, mesocarp, exocarp, and
 oil glands. The exocarps for each fruit were further processed, isolating
 the separate, low-density spots in its interior corresponding to the oil
 glands. Low density spots of less than 3x3x3 voxel size were deemed as
 noise and discarded. Similarly, low density spots 3 times larger than the
 median size were broken into smaller separate pieces or discarded if
 separation was not possible. The center of each oil gland was calculated
 as the center of mass of the voxels composing such gland.  An in-house
 \texttt{scipy.ndimage}-based python script was used to process the images
 for all fruits and their tissues.
description: All the scans are provided as single 3D 8-bit TIFF files which
 can be manipulated as 3D arrays. Point clouds representing the center of
 citrus oil glands are attached as well. These point clouds can be later
 used to model the whole fruit shape. Please read the
 README files included with the data for more details.