BackgroundHigh quality 3D information of the microscopic plant tissue morphology-the spatial organization of cells and intercellular spaces in tissues-helps in understanding physiological processes in a wide variety of plants and tissues. X-ray micro-CT is a valuable tool that is becoming increasingly available in plant research to obtain 3D microstructural information of the intercellular pore space and individual pore sizes and shapes of tissues. However, individual cell morphology is difficult to retrieve from micro-CT as cells cannot be segmented properly due to negligible density differences at cell-to-cell interfaces. To address this, deep learning-based models were trained and tested to segment individual cells using X-ray micro-CT images of parenchyma tissue samples from apple and pear fruit with different cell and porosity characteristics.ResultsThe best segmentation model achieved an Aggregated Jaccard Index (AJI) of 0.86 and 0.73 for apple and pear tissue, respectively, which is an improvement over the current benchmark method that achieved AJIs of 0.73 and 0.67. Furthermore, the neural network was able to detect other plant tissue structures such as vascular bundles and stone cell clusters (brachysclereids), of which the latter were shown to strongly influence the spatial organization of pear cells. Based on the AJIs, apple tissue was found to be easier to segment, as the porosity and specific surface area of the pore space are higher and lower, respectively, compared to pear tissue. Moreover, samples with lower pore network connectivity, proved very difficult to segment.ConclusionsThe proposed method can be used to automatically quantify 3D cell morphology of plant tissue from micro-CT instead of opting for laborious manual annotations or less accurate segmentation approaches. In case fruit tissue porosity or pore network connectivity is too low or the specific surface area of the pore space too high, native X-ray micro-CT is unable to provide proper marker points of cell outlines, and one should rely on more elaborate contrast-enhancing scan protocols.
机构:
KU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Janssen, Siem
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Verboven, Pieter
论文数: 0引用数: 0
h-index: 0
机构:
KU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Verboven, Pieter
;
Nugraha, Bayu
论文数: 0引用数: 0
h-index: 0
机构:
KU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Nugraha, Bayu
;
Wang, Zi
论文数: 0引用数: 0
h-index: 0
机构:
KU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Wang, Zi
;
Boone, Matthieu
论文数: 0引用数: 0
h-index: 0
机构:
UGent Ghent Univ, Ctr Xray Tomog, Proeftuinstr 86, B-9000 Ghent, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Boone, Matthieu
;
Josipovic, Ivan
论文数: 0引用数: 0
h-index: 0
机构:
UGent Ghent Univ, Ctr Xray Tomog, Proeftuinstr 86, B-9000 Ghent, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Josipovic, Ivan
;
Nicolai, Bart M.
论文数: 0引用数: 0
h-index: 0
机构:
KU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Flanders Ctr Postharvest Technol, Willem de Croylaan 42, B-3001 Leuven, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Univ Kansas, Dept Ecol & Evolutionary Biol, 2101 Constant Ave, Lawrence, KS 66047 USAUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Lehmeier, Christoph
;
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Pajor, Radoslaw
;
Lundgren, Marjorie R.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Lundgren, Marjorie R.
;
Mathers, Andrew
论文数: 0引用数: 0
h-index: 0
机构:
Univ Nottingham, Sch Biosci, Div Agr & Environm Sci, Sutton Bonington Campus, Loughborough LE12 5RD, Leics, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Mathers, Andrew
;
Sloan, Jen
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Sloan, Jen
;
Bauch, Marion
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Bauch, Marion
;
Mitchell, Alice
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Mitchell, Alice
;
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Bellasio, Chandra
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Green, Adam
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Phys & Astron, Hounsfield Rd, Sheffield S3 7RH, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Green, Adam
;
Bouyer, Daniel
论文数: 0引用数: 0
h-index: 0
机构:
CNRS, IBMP, UPR2357, 12 Rue Gen Zimmer, F-67084 Strasbourg, France
Ecole Normale Super, INSERM U1024, UMR8197, Inst Biol,ENS, 46 Rue Ulm, F-75230 Paris 05, FranceUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Bouyer, Daniel
;
Schnittger, Arp
论文数: 0引用数: 0
h-index: 0
机构:
CNRS, IBMP, UPR2357, 12 Rue Gen Zimmer, F-67084 Strasbourg, France
Univ Hamburg, Biozentrum Klein Flottbek, Dept Dev Biol, Ohnhorststr 18, D-22609 Hamburg, GermanyUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Schnittger, Arp
;
Sturrock, Craig
论文数: 0引用数: 0
h-index: 0
机构:
Univ Nottingham, Sch Biosci, Div Agr & Environm Sci, Sutton Bonington Campus, Loughborough LE12 5RD, Leics, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Sturrock, Craig
;
Osborne, Colin P.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Osborne, Colin P.
;
Rolfe, Stephen
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Rolfe, Stephen
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Mooney, Sacha
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Fleming, Andrew J.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
机构:
Katholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Naets, M.
;
Wang, Z.
论文数: 0引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Wang, Z.
;
Verboven, P.
论文数: 0引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Verboven, P.
;
Nicolai, B.
论文数: 0引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Flanders Ctr Postharvest Technol VCBT, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Nicolai, B.
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Keulemans, W.
论文数: 0引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Div Crop Biotech, Dept Biosyst BOISYST, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Keulemans, W.
;
Geeraerd, A.
论文数: 0引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
机构:
KU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Janssen, Siem
;
Verboven, Pieter
论文数: 0引用数: 0
h-index: 0
机构:
KU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Verboven, Pieter
;
Nugraha, Bayu
论文数: 0引用数: 0
h-index: 0
机构:
KU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Nugraha, Bayu
;
Wang, Zi
论文数: 0引用数: 0
h-index: 0
机构:
KU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Wang, Zi
;
Boone, Matthieu
论文数: 0引用数: 0
h-index: 0
机构:
UGent Ghent Univ, Ctr Xray Tomog, Proeftuinstr 86, B-9000 Ghent, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Boone, Matthieu
;
Josipovic, Ivan
论文数: 0引用数: 0
h-index: 0
机构:
UGent Ghent Univ, Ctr Xray Tomog, Proeftuinstr 86, B-9000 Ghent, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Josipovic, Ivan
;
Nicolai, Bart M.
论文数: 0引用数: 0
h-index: 0
机构:
KU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
Flanders Ctr Postharvest Technol, Willem de Croylaan 42, B-3001 Leuven, BelgiumKU Leuven Univ Leuven, Div BIOSYST MeBioS, Postharvest Grp, Willem de Croylaan 42, B-3001 Leuven, Belgium
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Univ Kansas, Dept Ecol & Evolutionary Biol, 2101 Constant Ave, Lawrence, KS 66047 USAUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Lehmeier, Christoph
;
论文数: 引用数:
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机构:
Pajor, Radoslaw
;
Lundgren, Marjorie R.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Lundgren, Marjorie R.
;
Mathers, Andrew
论文数: 0引用数: 0
h-index: 0
机构:
Univ Nottingham, Sch Biosci, Div Agr & Environm Sci, Sutton Bonington Campus, Loughborough LE12 5RD, Leics, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Mathers, Andrew
;
Sloan, Jen
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Sloan, Jen
;
Bauch, Marion
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Bauch, Marion
;
Mitchell, Alice
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Mitchell, Alice
;
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机构:
Bellasio, Chandra
;
Green, Adam
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Phys & Astron, Hounsfield Rd, Sheffield S3 7RH, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Green, Adam
;
Bouyer, Daniel
论文数: 0引用数: 0
h-index: 0
机构:
CNRS, IBMP, UPR2357, 12 Rue Gen Zimmer, F-67084 Strasbourg, France
Ecole Normale Super, INSERM U1024, UMR8197, Inst Biol,ENS, 46 Rue Ulm, F-75230 Paris 05, FranceUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Bouyer, Daniel
;
Schnittger, Arp
论文数: 0引用数: 0
h-index: 0
机构:
CNRS, IBMP, UPR2357, 12 Rue Gen Zimmer, F-67084 Strasbourg, France
Univ Hamburg, Biozentrum Klein Flottbek, Dept Dev Biol, Ohnhorststr 18, D-22609 Hamburg, GermanyUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Schnittger, Arp
;
Sturrock, Craig
论文数: 0引用数: 0
h-index: 0
机构:
Univ Nottingham, Sch Biosci, Div Agr & Environm Sci, Sutton Bonington Campus, Loughborough LE12 5RD, Leics, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Sturrock, Craig
;
Osborne, Colin P.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Osborne, Colin P.
;
Rolfe, Stephen
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
Rolfe, Stephen
;
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机构:
Mooney, Sacha
;
Fleming, Andrew J.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, EnglandUniv Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England
机构:
Katholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Naets, M.
;
Wang, Z.
论文数: 0引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Wang, Z.
;
Verboven, P.
论文数: 0引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Verboven, P.
;
Nicolai, B.
论文数: 0引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Flanders Ctr Postharvest Technol VCBT, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Nicolai, B.
;
Keulemans, W.
论文数: 0引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Div Crop Biotech, Dept Biosyst BOISYST, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium
Keulemans, W.
;
Geeraerd, A.
论文数: 0引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, BelgiumKatholieke Univ Leuven, Div MoBioS, Dept Biosyst BIOSYST, Willem de Croylaan 42, B-3001 Leuven, Belgium