Automatic 3D cell segmentation of fruit parenchyma tissue from X-ray micro CT images using deep learning

Van Doorselaer, Leen; Verboven, Pieter; Nicolai, Bart

doi:10.1186/s13007-024-01137-y

Plant Methods

Table 1 Morphometric parameters of the cell matrix and pore space of three tissue samples (mean ± SD) per cortex position and pome fruit cultivar

From: Automatic 3D cell segmentation of fruit parenchyma tissue from X-ray micro CT images using deep learning

Parameter	Cortex	‘Celina’	‘Conference’	‘Fred’	‘Braeburn’	‘Jonagold’	‘Kizuri’
Cell density [mm⁻³]	Inner	652 ± 169^Aa	837 ± 189^Aa	1005 ± 205^Aa	221 ± 40^Ab	187 ± 41^Ab	258 ± 45^Ab
	Middle	606 ± 75^Ba	652 ± 103^Ba	593 ± 193^Ba	224 ± 10^Bb	172 ± 32^Bb	197 ± 49^Bb
	Outer	743 ± 325^Ba	626 ± 71^Ba	695 ± 244^Ba	183 ± 10^Bb	162 ± 42^Bb	215 ± 61^Bb
Stone cell density [mm⁻³]	Inner	1.96 ± 1.43^a	1.23 ± 0.12^b	0.87 ± 0.00^b	–	–	–
	Middle	2.83 ± 0.78^a	1.16 ± 0.33^b	1.38 ± 0.33^b	–	–	–
	Outer	3.33 ± 1.38^a	1.88 ± 0.45^b	1.01 ± 0.25^b	–	–	–
Stone cell volume fraction [%]	Inner	0.45 ± 0.50	0.42 ± 0.15	1.49 ± 1.26	–	–	–
	Middle	0.66 ± 0.56	0.72 ± 0.77	0.85 ± 0.48	–	–	–
	Outer	0.35 ± 0.14	0.45 ± 0.22	0.81 ± 0.63	–	–	–
Vascular tissue volume fraction [%]	Inner	0.21 ± 0.36	0 ± 0	0.71 ± 1.22	0.11 ± 0.11	0.08 ± 0.13	0.59 ± 0.31
	Middle	0.04 ± 0.04	0 ± 0	0 ± 0	0.05 ± 0.05	0 ± 0	0 ± 0
	Outer	1.28 ± 1.21	0.64 ± 1.06	1.64 ± 2.85	0.05 ± 0.05	0.08 ± 0.13	0.11 ± 0.20
Cell matrix anisotropy	Inner	0.007 ± 0.001^b	0.005 ± 0.001^b	0.008 ± 0.001^b	0.037 ± 0.002^a	0.036 ± 0.021^a	0.047 ± 0.007^a
	Middle	0.005 ± 0.002^b	0.008 ± 0.004^b	0.010 ± 0.002^b	0.019 ± 0.007^a	0.014 ± 0.009^a	0.025 ± 0.011^a
	Outer	0.015 ± 0.013^b	0.007 ± 0.004^b	0.006 ± 0.002^b	0.022 ± 0.004^a	0.030 ± 0.015^a	0.028 ± 0.012^a
Cell matrix specific surface area [mm⁻¹]	Inner	15.13 ± 1.38^ab	13.36 ± 2.48^bc	12.78 ± 2.68^c	13.93 ± 1.07 ^bc	15.91 ± 1.06^a	15.85 ± 0.56^a
	Middle	15.27 ± 0.79^ab	13.39 ± 1.84 ^bc	11.45 ± 1.06^c	14.46 ± 0.01 ^bc	15.37 ± 0.56^a	15.51 ± 1.29^a
	Outer	14.74 ± 1.93^ab	13.34 ± 1.74 ^bc	10.07 ± 0.58^c	13.21 ± 0.33 ^bc	16.94 ± 1.21^a	16.08 ± 1.28^a
Porosity [%]	Inner	5.09 ± 1.09^c	4.48 ± 1.27^c	3.29 ± 0.53^d	16.35 ± 1.47^b	19.14 ± 1.20^a	19.29 ± 0.98^a
	Middle	5.05 ± 0.42^c	4.90 ± 1.39^c	3.87 ± 0.94^d	16.11 ± 0.70^b	20.84 ± 4.75^a	22.34 ± 3.40^a
	Outer	4.82 ± 0.18^c	4.86 ± 1.28^c	2.98 ± 0.54^d	17.49 ± 0.93^b	26.73 ± 1.13^a	22.11 ± 2.77^a
Pore density [mm⁻³]	Inner	2692 ± 1226^Aa	3732 ± 495^Aa	4784 ± 1534^Aa	211 ± 120^Ab	221 ± 39^Ab	295 ± 61^Ab
	Middle	3189 ± 646^ABa	3322 ± 366^ABa	2735 ± 1315^ABa	249 ± 80^ABb	147 ± 62^ABb	139 ± 75^ABb
	Outer	3271 ± 1954^Ba	2860 ± 1092^Ba	2995 ± 467^Ba	138 ± 17^Bb	102 ± 57^Bb	171 ± 78^Bb
Pore space anisotropy	Inner	0.12 ± 0.02^ab	0.08 ± 0.01^ab	0.23 ± 0.07^a	0.16 ± 0.01^ab	0.14 ± 0.07^b	0.22 ± 0.04^ab
	Middle	0.09 ± 0.04^ab	0.16 ± 0.11^ab	0.23 ± 0.05^a	0.10 ± 0.04^ab	0.08 ± 0.06^b	0.09 ± 0.04^ab
	Outer	0.23 ± 0.16^ab	0.14 ± 0.09^ab	0.19 ± 0.07^a	0.10 ± 0.02^ab	0.08 ± 0.04^b	0.10 ± 0.06^ab
Pore space specific surface area [mm⁻¹]	Inner	228 ± 29^Aa	219 ± 15^Aa	227 ± 36^Aa	60 ± 11^Ab	58 ± 3^Ab	57 ± 1^Ab
	Middle	228 ± 17^ABa	203 ± 27^ABa	209 ± 27^ABa	64 ± 4^ABb	52 ± 13^ABb	48 ± 9^ABb
	Outer	231 ± 44^Ba	203 ± 22^Ba	225 ± 24^Ba	52 ± 2^Bb	42 ± 5^Bb	50 ± 8^Bb
Euler number	Inner	− 1202 ± 2666^c	5761 ± 795^a	9829 ± 2872^a	1475 ± 646^b	924 ± 287^bc	1934 ± 395^b
	Middle	− 733 ± 1076^c	4384 ± 2609^a	5638 ± 1877^a	1577 ± 588^b	728 ± 426^bc	1015 ± 262^b
	Outer	1274 ± 1925^c	4654 ± 1595^a	5939 ± 2287^a	1023 ± 226^b	479 ± 232^bc	1345 ± 575^b

Different upper case characters in the same column for each parameter indicate significant differences (p < 0.05) at different cortex position for the same cultivar. Different lower case characters in the same row indicate significant differences (p < 0.05) among different cultivars for the same cortex position

Back to article page

ISSN: 1746-4811

Contact us

Submission enquiries: journalsubmissions@springernature.com