Journal of Experimental Botany Advance Access published August 11, 2015

Journal of Experimental Botany

doi:10.1093/jxb/erv387
This paper is available online free of all access charges (see http://jxb.oxfordjournals.org/open_access.html for further details)

RESEARCH PAPER

X-ray computed tomography to study rice (Oryza sativa L.)

panicle development
Vibhuti M.Jhala and Vrinda S.Thaker*
Plant Biotechnology and Molecular Biology Laboratory, Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat,
India

Received 20 February 2015; Revised 21 July 2015; Accepted 24 July 2015

Editor: ChrisHawes

Abstract
Computational tomography is an important technique for developing digital agricultural models that may help farmers and breeders for increasing crop quality and yield. In the present study an attempt has been made to understand
rice seed development within the panicle at different developmental stages using this technique. During the first
phase of cell division the Hounsfield Unit (HU) value remained low, increased in the dry matter accumulation phase,
and finally reached a maximum at the maturation stage. HU value and seed dry weight showed a linear relationship
in the varieties studied. This relationship was confirmed subsequently using seven other varieties. This is therefore
an easy, simple, and non-invasive technique which may help breeders to select the best varieties. In addition, it may
also help farmers to optimize post-anthesis agronomic practices as well as deciding the crop harvest time for higher
grain yield.
Key words: CT scanning, Hounsfield unit (HU), rice (Oryza sativa L.).

Introduction
Rice (Oryza sativa L.) is an important food crop for over half
the human population. Breeding for better quality and highyield is the main focus of rice geneticists and breeders. There
is a great demand for improving grain quality and quantity
to meet the requirements of an increasing world population.
Understanding the fundamental genetic factors that control rice yield, together with supporting the breeders ability
to manipulate such factors, would be an added advantage
for ensuring an adequate global food supply. The number
of seeds per panicle is believed to be the most plastic yield
component, whereas the panicle number and individual seed
weight are under more rigid genetic control (Zhikang etal.,

1997; Luo etal., 2001). Yield in rice can be calculated as the

number of seeds per panicle, the size of seeds, the number of
panicles per plant, and the number of plants per hectare. The
arrangement of seeds in a panicle is central to the growth of
the seeds and the yield of the crop. Many agronomical and/
or physiological studies have been conducted to judge the
varietal potential of different plants and the correlation of
growth parameters in yield determination (Koutroubas and
Ntanos, 2003; Prasad etal., 2006; Li etal., 2012). These studies give a reasonable understanding of seed development and
yield determination; however, they are time-consuming and
require tedious methodologies. In addition, the separation

Abbreviations: CT, computational tomography; DAF, days after flowering; DMA, dry matter accumulation; HU, Hounsfield unit; MPR, Multi-Planar Reformatting;
W/L, window/level.
The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Downloaded from http://jxb.oxfordjournals.org/ at Department of Poultry Science, BAU on October 6, 2015

* To whom correspondence should be addressed. E-mail: thakervs@gmail.com

Page 2 of 7 | Jhala and Thaker

Materials and methods

Plant sampling
Two hybrid varieties of rice (Oryza sativa), PAC801 and PAC807,
were grown and maintained at the Vikram farm, Vapi, Gujarat
(20.3667N, 72.9000E). The former is higher yielding compared
with the latter. The normal cultural practices such as irrigation, the
applications of fertilizers, insecticides, pesticides etc. were conducted
to optimize the yield. On the day of anthesis, uniformly growing
panicles were tagged for each variety and harvested at the desired
periods. The number of panicles per plant and plant height were
noted for 100 plants and the mean values standard deviation (SD)
are shown here.

Growth analysis
For the measurement of fresh and dry weights, the tagged panicles were harvested at weekly intervals. The seeds were separated,
counted, and weighed before and after oven-drying at 60C until a
constant weight was recorded. Seed water content was calculated by
differences in fresh and dry weights. Data were collected in triplicate
and the mean dry weights and water content are reported. The data
were fitted to polynomial equations for a best-fit curve for each data
set. Changes in the value per unit time were calculated as rate for a
parameter and plotted against days after flowering (DAF). ANOVA
(single factor) was performed for data on dry matter accumulation
(DMA) and water content.
Computational tomography (CT) scanning
CT scanning technology, routinely used with X-rays to visualize thin
cross-sections of an organ, was used here for rice panicles. X-rays
are generated from a source located to one side of the gantry, attenuated through the panicle, and then registered by a series of detectors placed on the opposite side of the panicle. Both X-ray source
and detectors make a synchronous movement around the panicle so
that all angles of measurement are covered. As the X-ray penetrates
through a panicle, some X-rays are absorbed. The higher the density
of a part of the panicle, the higher is its X-ray absorption.
In a preliminary experiment, a set of scanning configuration
parameters was optimized for standardization (see Supplementary
Fig. S1 at JXB online). In the first season, the growth stages were
determined and standardized for the CT scanning procedure. In the
second season, the HU value and growth were determined for the
two varieties and their relationship was developed. This relationship
was further confirmed with seven other varieties by measuring CT
scan parameters at maturity stage.
Image collection
Panicles from the two rice varieties, collected at different developmental stages, i.e. initial cell division (5 d), milky white (10 d), dry
matter accumulation (15 d), and maturation stage (25 d), were subjected to CT scanning.
No special preparation of the samples was required for CT scanning. The collected panicles of both varieties were scanned individually in a Philips high-resolution medical CT scanner (GE Medical
Merge), installed at a private Medical Centre: Prabhat CT Scanning
Hospital, Rajkot, India. The images collected were visualized in CT
scan software eFilmLite. The window/level (W/L) adjustment for
rice panicles was the first step for proper visualization of the images.
The panicles were best observed in 1500/600 (lungs Window/level).
All the scanned images were pre-processed in the Merge Healthcare
CT scanner software utilizing the Multi-Planar Reformatting
(MPR) parameter (Instrument software). Sagittal (dividing into left
and right pieces) and coronal (dividing into anterior and posterior
pieces) Multi-Planar Reformatting (MPR) provides easier visualization by projecting two orthogonal viewing planes from a 2-D image.
The MPR tool gives an arbitrary perpendicular viewing plane from
a 2-D image. By using the MPR, different views were created and
used for determining Hounsfield unit (HU), for panicle length and
seed size measurement.
Hounsfield unit (HU) and seed size determination
The cross-sectional images constructed from the CT scan data are
maps of CT numbers (CTN), which are an average of the relative
measurement of the pixel density in the image, also known as the
corresponding volume or voxel. The CTN values are calculated
using the X-ray linear attenuation coefficient, and the unit of CTN
is the Hounsfield unit (HU), briefly calculatedas,

CTN (HU ) = object water / object air 1000

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of seeds from the panicle, followed by an estimation of seed

size and position within panicle restrict the sample size for an
evaluation of cropyield.
High through-put, non-destructive phenotyping methods
provide an opportunity to analyse the growth and development of plants with accuracy and speed (Yang etal., 2013,
Humplk et al., 2015). High-resolution X-ray computed
tomography (CT) scanning has the possibility of visualizing
the panicle in 3-D space in situ because it is a non-invasive
and non-destructive procedure (Kalender, 2000). In addition,
continuous sectioning of an object can be skeletonized into
2-D images for detailed analysis. In many plant experiments,
the CT scanned data are used to study root architecture in
soil that may help researchers to understand root growth and
development in relation to its geological conditions (Grose
etal., 1996; Moradi etal., 2011; Schluter etal., 2010).
Rice functional genomic research using various genomic
tools is a prime focus because of its importance for understanding a model monocot genome. In addition, in order to
fill the gaps between genomic analysis and breeding for better
quality high-yielding rice, automated phenotyping methods
are required to replace the currently practised manual ones
(Duan etal., 2011). In recent years, the number of tillers per
plant have been calculated using CT scanning in rice (Yang
etal., 2011). However, to the best of our knowledge, no such
study for panicle development has been reported. Rice panicle development over time was studied here using CT scan
technology to understand yield potential in rice together with
exploring its use for the best possible agriculture practices.
Two rice varieties were selected that differed in their final
yield in order to understand how the CT scan parameters
are related to the yield difference. These data were upgraded
and analysed by other optional analytical procedures and the
results for two rice varieties at different developmental stages
are reported. The CT scanning configurations were adjusted
to optimize data collection for the different stages from initial
seed setting to the mature seed. The procedures to construct
a 3-D image of the panicle from the CT scan data, which
were then skeletonized to 2-D images, are described. Briefly,
an attempt was made to observe a correlation between the
HU value and growth parameters using X-ray computation
tomography of the rice panicle. This correlation was substantiated by similar analyses in seven different rice varieties at
maturity. It is hoped that this approach may act as a guide for
deciding the appropriate harvest time.

X-ray computed tomography of rice panicle | Page 3 of 7

Dry weight (mg)

25.0
20.0
15.0
10.0
5.0
0.0

20
Day after flowering

PAC 801
Poly. (PAC 801)

30

40

PAC 807
Poly. (PAC 807)

PAC 801
1.60

12.00
10.00

1.20

8.00

0.80

6.00
4.00

0.40
0.00

2.00
0

10

20

30

0.00

Day after flowering

DRY WGT RATE

FIT WC

PAC 807
12.00

10.00

1.6

8.00

1.2

6.00
0.8

4.00

0.4
0

Table1. Yield component data of two rice varieties

10

Water content

The plant heights of PAC801 and PAC807 were almost equal

at 125130 cm: however, the duration of vegetative growth
was longer (20 d) in PAC801 than in PAC807. In PAC801,
the number of seeds per panicle was also greater (170215)
than in PAC807 (165200). In addition, the number of tillers was greater in PAC801 (3032) than in PAC807 (2530)
(Table1). At a given time, if the number of plants per unit
area was equal, the final yield was higher in PAC801. Data of
seed dry weight and water content were fitted to polynomial
equations of different degrees, and the best-fit equation was
determined statistically by performing a t test for different r2
values. The data on DMA were adequately explained by a
3rd degree polynomial equation (Fig.1A). Seed dry weight,
started accumulating after fertilization, and entered the linear
phase of DMA up to 30 DAF. Maximum DMA was recorded
in PAC801 (27mg) and PAC807 (21mg) on 28 DPF. In subsequent periods, no significant change in DMA was observed
in both varieties.
The rate of DMA per day reached a maximum on day 5 in
both varieties and declined thereafter. The declining trend was
very sharp in PAC807, whereas in PAC801 the value remained

30.0

Water content

Growth analysis

35.0

Dry weight rate

Results and discussion

2.00

10

20

30

0.00

Day after flowering

Characters

PAC-801

PAC-807

Grain yield (tn/ht)

Height (cm) n=10
No. of seeds/spike n=10
No. of tillers/plant n=10
Seed weight (mg) n=200

10.1764
1244
192.545
311
33.13

9.9788
121.53.5
182.535
27.52.5
31.9

DRY WGT RATE

FIT WC

Fig.1. (A) Change in mg dry weight. (B) Water content (WC) and rate
of dry matter accumulation (DMA) in variety PAC801 and (C) PAC807
against seed age in days. Each data point represents the mean value of
25 replicates at a given age; represents the standard deviation of the
sample or otherwise within the symbols.

Downloaded from http://jxb.oxfordjournals.org/ at Department of Poultry Science, BAU on October 6, 2015

Pseudo-colouring ofimages
ImageJ ver.1.46 software (http://imagej.nih.gov/ij) was used for the
pseudo-colouring of all the images. The pseudo-colouring option of
the software (the application of 16 colours) was applied for a better
visualization of the panicles. Apseudo-colour (or indexed colour)
image is a single channel grey image (8-, 16-, or 32-bit) that has colour assigned to it via a look-up table in ImageJ. The grey values of
ImageJ match red, green, and blue values in such a way that the
shades of grey are displayed as coloured pixels: 8-bit grey-coloured
images were turned into a 16-colour image in order of their developmental stages.

higher up to 18 d and declined thereafter (Fig. 1B, C).

The rate of dry matter accumulation is one of the parameters that determine the final yield (Bewley and Black, 1985).

Dry weight rate

Where, object is the mean value of linear attenuation coefficient for

the voxel; water is the linear attenuation coefficient of pure water;
and air is that of a standardized air sample (Kalender, 2000). The
CTN scale is linear and has a central axis at 0, which corresponds to
water, while air has the calibrated value of 1 000 HU. Hence, for the
CTN values, the intensities received by the detectors are expressed in
the linear Hounsfield unit (HU) scale for which typical values are 1
000 for air and 0 forwater.
The CTN values were derived for each processed image scan.
Each panicle was divided into three equal zones; upper, middle, and
lower. Atotal of 100 seeds from each scan were used for HU value
and the calculation of seed size. The measurement of seed size was
done using the in-built MPR tools (see Supplementary Figs S2 and
S3 at JXB online).

Page 4 of 7 | Jhala and Thaker

Calculation of HUvalue
The CT scanned images were opened in the MRP software
for further analysis. In the first screening, a total of 10 images
was selected from the centre for detailed analysis. In rice
panicles, grain development is asynchronous (Mohapatra
et al., 1993; Ishimaru et al., 2003). The degree and rate of
grain filling among spikelets can be very different according to their position on a panicle. Thus from the images, the
seeds were selected from the upper, middle, and lower parts
(see Supplementary Fig. S2 at JXB online). The CTN scale
was linear and centred on 0 (zero) which corresponds to
water. Positive and negative values represent matter denser
and less dense than water, respectively. Air has a calibrated

CTN value of 1 000 HU. One image is generated from a

single 512512 matrix of CTNs for a given interval along
the subject. The image represents the cross-sectional volume
PAC801
A

PAC807
E

Table2. Image collection from two rice varieties at stages of

developing seeds
CT scan conditions: voltage at 120kV, current 50 mA, scanning
thickness 1.5mm, voxel 0.2621mm3, Mode Tomo and child head
programme.
Stages

Initiation Elongation Dry matter

Maturation
accumulation

Scan spike length (cm) 10

Image numbers:
144
PAC-801
PAC-807
173

12
216

20
201

22
287

173

287

344

Fig.2. Spikelet images of rice varieties PAC801 (AD) and PAC807 (EH),
at the initiation (A, E), elongation (B, F), dry matter accumulation (C, G), and
maturation (D, H) phases, respectively. CT scan image is in the Multi-Planar
Reformatting (MRP) tool to visualize images for calculating various topological
parameters (for other details see Supplementary Fig. S1 at JXB online).

Downloaded from http://jxb.oxfordjournals.org/ at Department of Poultry Science, BAU on October 6, 2015

Data on water content revealed a gradual increase in both

the varieties, but initially a higher value was observed in
PAC801. The maximum value was almost similar (12mg)
in both. However, like the rate of DMA, the duration was
longer in PAC801 than PAC807 (Fig.1B, C). Water status has
been reported to play an important role in the development
of cotton (Rabadia et al., 1999), wheat seeds (Chanda and
Singh, 1998), soybean and other crops (Egli, 1990; Egli and
Tekrony, 1997). In cereal crops, grain-filling is a critical and
dynamic process that determines the final grain yield (Borra
and Westgate, 2006). Seed filling is sensitive to water shortages as the water relations of the developing seed plays a fundamental role in seed filling (Schnyder and Baum, 1992).
In this experiment, single factor ANOVA for DMA and
WC data of both the varieties were statistically significant;
although that of PAC801 were more significant (P 0.001)
than PAC807 (P 0. 01). From these data analyses, rice seed
development was divided into (i) a cell division phase (05 d),
(ii) a cell elongation/milky stage (512 d), (iii) DMA (1025
d), and (iv) a maturation phase (25 d onward).
Panicles of rice were scanned separately for PAC801 and
PAC807 at the four stages. The panicle was placed on the
bed of the CT scanner and moved vertically through the
X-ray plane under the conditions described earlier (Table2).
Atotal of 177344 images for PAC801 and 144287 images
for PAC807 were generated covering 10cm (initial) to 25cm
(mature) panicle length of the respective varieties. Images
were placed in a 2-D view of the complete panicle and 10
images were selected from the centre (Fig.2; Table2).

X-ray computed tomography of rice panicle | Page 5 of 7

of the subject. Accordingly, a CT image is a map of relative density (Kalender, 2000). There is a direct relationship
between CTN and material density. From these images of
panicles, 100 seeds were used for the HU value and the determination of seed size. Mean HU values and size were calculated in all three parts of both the varieties for the different
developmental stages (Fig.3). More negative HU values were
observed during the early stage of seed development and
moved towards more positive when seeds reached maturity.
This pattern was similar in both the varieties. In addition, little difference was observed in HU value with position on the
panicle. The value ranged from 200 to 750 in the rice varieties studied. At the time of seed set, water content decreased

with seed maturation; and when the seed DMA stabilized, the
water content was negligible (Fig. 1B, C). Thus the pattern
of HU value and seed water content also showed a relationship. Asimilar decrease in water content with wood density
and HU value has been reported by Wu et al. (2011). The
data analysed for HU value and seed dry weight using single factor ANOVA also showed statistically significant results
(P 0.001) for both varieties. The principal advantage of a
direct relationship between HU value and water content is
that it can be used to understand the seed water status during the developmental stages which is a guiding point for the
time of harvest and for fertilizer application, which is a tedious process to estimate manually. It has been demonstrated
UPPER
MIDDLE
BOTTOM

0.00

HU Value

-200.00
-400.00
-600.00
-800.00
-1000.00

Initiation

Elongation

Dry matter
accumulation

Maturation

Growth stages

PAC-807
0.00

UPPER
MIDDLE
BOTTOM

HU Value

-200.00

-400.00

-600.00

-800.00

-1000.00

Initiation

Elongation

Dry matter
accumulation

Maturation

Growth stages
Fig.3. Changes in HU value in PAC801 (A) and PAC807 (B) at different growth stages of the seed: (1) initiation, (2) elongation, (3) dry matter
accumulation, and (4) maturation. The upper, middle, and bottom bars indicate the position of the seeds on the panicle from the top to the bottom,
respectively. The vertical bars represent std of the mean of 100 replicates.

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PAC-801

Page 6 of 7 | Jhala and Thaker

A

log dryweight

1.5

0.5

y = 1.3176x - 2.2232
R = 0.9108
2

2.2

2.4

2.6

2.8

log (1000+HU)

1.45

log dryweight

1.35
1.3
y = 5.239x - 13.72
R = 0.942

1.25
1.2
2.85

2.86

2.87
log(1000+HU)

2.88

2.89

Fig.4. (A) Pooled linear relationship between mean log dry matter
accumulation versus log (1 000+HU value) at different growth stages of
seed development in PAC801 and PAC807, rice varieties (n=200). (B)
Linear relationship between mean log dry matter accumulation versus log
(1 000+HU value) in seeds of seven different rice varieties (n=175); other
details as in Table1.

Conclusion
In the present study, CT scanning has been used to analyse
rice panicle development in two rice varieties that differ in
their yield potential. The HU value showed a close correlation

PAC801

Initiation

Elongation

Dry matter
accumulation

Maturation
Stages with
colour bar

PAC807

Fig.5. Pseudo-colouring effect on the 8-bit binary CT scan images of PAC801 and PAC807 with developmental stages by using ImageJ software.
Changes from the blue to the red scales indicate changes in water content and dry matter at the different stages of seed development. (The stronger the
blue colour, the higher the seed water content; the stronger the red colour, the higher the dry matter accumulation in the seed.)

Downloaded from http://jxb.oxfordjournals.org/ at Department of Poultry Science, BAU on October 6, 2015

1.4

in a number of studies that water content and seed dry matter accumulation rate are directly correlated (Rabadia etal.,
1999; Egli and Tekrony, 1997). Since the amount of water is
also related to the rate of dry matter accumulation in the rice
varieties in the present study and elsewhere, it should also
provide information for screening better yielding varieties for
the breeders.
In particular, HU values and seed dry weight data can be
better explained by a linear relationship of log (1 000+HU
value) versus log dry weight data. The calculation for dry
weight at different growth phases and their respective HU values showed a linear relationship (Fig.4A; r2=0.910, n=800).
The above experiment was repeated with seven other rice
varieties which also showed the linear relationship (Fig.4B;
r2=0.942, n=175), thus the authors believe that it may help
breeders to screen for promising rice varieties.
Pseudo-colouring simulates the architecture of seed
development studies as well as their image analysis with the
developmental stages. It is easy to trace more or less densely
packed seeds in the panicle by viewing the contrasting images
(Fig.5). This pseudo colouring approach could further help
in evaluating good varieties. The changes in colour pattern,
i.e. initially blue to yellow-red, indicates that water content
decreases with seed age and this may help to predict harvest
time and seed density.

X-ray computed tomography of rice panicle | Page 7 of 7

Supplementarydata
Supplementary data are available at JXB online.
A schematic diagram of CT scan procedure for rice panicle.
Figure S1. (A) eFilmLite CT scan software, (B) W/L (window / level) adjustment, (C) MPR (MultiPlanar Reformatting)
tool and (D) Series of sections observed and Export selected
image.
Figure S2. Calculation of HU value from the MPR images,
(A) PAC801 and (B) PAC807. Rice panicle axis divided
equally in to three part: upper, middle and lower in both the
varieties (individual white portion in Figure indicates seeds).
Figure S3. Seed size measurement in eFilmLite CT software (A) PAC801and (B) PAC 807.
Table S1. Seven rice varieties used in study.

Acknowledgements
The authors are very grateful to Dr Navinbhai Patel and Dr Nisha Patel,
Prabhat CT Scanning Hospital, Rajkot for their technical support and to Dr
PP Vaishnav for fruitful discussion. The authors also thank Vikram Farm,
UPL Vapi, Gujarat, for the supply of plant materials.

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between water content and dry matter accumulation in seeds

at different developmental stages. The correlation between
HU values from CT scans and seed development in the panicle suggests that this technique could be useful for farmers
and breeders. For example, CT scanning, together with the
pseudo-colour development method, can help to understand
plant demand during the post-anthesis period. The HU value
may be taken as a marker to improve agricultural practices
such as irrigation, the application of growth-promoting substances, and developmental status at harvest time and so may
help farmers to decide when to harvest the standing crop. All
this is possible in a predictable and non-invasive manner. In
addition, it is also hoped that this technique may help variety
selection in breeding programmes. The authors are aware of
the fact that the usefulness of this technique in variety selection requires more work in terms of larger data sets of different varieties and may, perhaps, require some modification of
the technique in order to develop a robust system. This will be
the focus of our future work.