10.5061/DRYAD.34TMPG4N6
Amezquita, Erik J.
0000-0002-9837-0397
Michigan State University
Quigley, Michelle Y.
0000-0001-5436-6532
Michigan State University
Ophelders, Tim
Utrecht University
Seymour, Danelle
0000-0003-2250-8377
University of California, Riverside
Munch, Elizabeth
0000-0002-9459-9493
Michigan State University
Chitwood, Daniel H.
0000-0003-4875-1447
Michigan State University
Data from: The shape of aroma: Measuring and modeling citrus oil gland
distribution
Dryad
dataset
2022
FOS: Biological sciences
computed tomography (CT) x-ray
X-ray computed tomography
Citrus
Fruit Morphology
3-D shape
National Institute of Food and Agriculture
https://ror.org/05qx3fv49
Michigan State University
https://ror.org/05hs6h993
National Science Foundation
https://ror.org/021nxhr62
CCF-1907591
National Science Foundation
https://ror.org/021nxhr62
CCF-2106578
National Science Foundation
https://ror.org/021nxhr62
CCF-2142713
University of California, Riverside
https://ror.org/03nawhv43
Michigan State University
https://ror.org/05hs6h993
2022-05-12T00:00:00Z
2022-05-12T00:00:00Z
en
https://github.com/amezqui3/citrus_morphology
https://doi.org/10.1002/ppp3.10333
39655191178 bytes
6
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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)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.
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.