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Items: 42

1.

Recovering Wind-induced Plant Motion in Dense Field Environments via Deep Learning and Multiple Object Tracking.

Gibbs JA, Burgess AJ, Pound MP, Pridmore TP, Murchie EH.

Plant Physiol. 2019 Jul 22. pii: pp.00141.2019. doi: 10.1104/pp.19.00141. [Epub ahead of print]

2.

A convolutional neural network for fast upsampling of undersampled tomograms in X-ray CT time-series using a representative highly sampled tomogram.

Bellos D, Basham M, Pridmore T, French AP.

J Synchrotron Radiat. 2019 May 1;26(Pt 3):839-853. doi: 10.1107/S1600577519003448. Epub 2019 Apr 23.

3.

Active Vision and Surface Reconstruction for 3D Plant Shoot Modelling.

Gibbs JA, Pound M, French A, Wells D, Murchie E, Pridmore T.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Apr 25. doi: 10.1109/TCBB.2019.2896908. [Epub ahead of print]

PMID:
31027044
4.

Plant Phenotyping: An Active Vision Cell for Three-Dimensional Plant Shoot Reconstruction.

Gibbs JA, Pound M, French AP, Wells DM, Murchie E, Pridmore T.

Plant Physiol. 2018 Oct;178(2):524-534. doi: 10.1104/pp.18.00664. Epub 2018 Aug 10.

5.

Erratum to: Deep machine learning provides state-of-the-art performance in image-based plant phenotyping.

Pound MP, Atkinson JA, Townsend AJ, Wilson MH, Griffiths M, Jackson AS, Bulat A, Tzimiropoulos G, Wells DM, Murchie EH, Pridmore TP, French AP.

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy042. No abstract available.

6.

Author Correction: Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate.

Giri J, Bhosale R, Huang G, Pandey BK, Parker H, Zappala S, Yang J, Dievart A, Bureau C, Ljung K, Price A, Rose T, Larrieu A, Mairhofer S, Sturrock CJ, White P, Dupuy L, Hawkesford M, Perin C, Liang W, Peret B, Hodgman CT, Lynch J, Wissuwa M, Zhang D, Pridmore T, Mooney SJ, Guiderdoni E, Swarup R, Bennett MJ.

Nat Commun. 2018 May 1;9(1):1810. doi: 10.1038/s41467-018-04280-y.

7.

Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate.

Giri J, Bhosale R, Huang G, Pandey BK, Parker H, Zappala S, Yang J, Dievart A, Bureau C, Ljung K, Price A, Rose T, Larrieu A, Mairhofer S, Sturrock CJ, White P, Dupuy L, Hawkesford M, Perin C, Liang W, Peret B, Hodgman CT, Lynch J, Wissuwa M, Zhang D, Pridmore T, Mooney SJ, Guiderdoni E, Swarup R, Bennett MJ.

Nat Commun. 2018 Apr 12;9(1):1408. doi: 10.1038/s41467-018-03850-4. Erratum in: Nat Commun. 2018 May 1;9(1):1810.

8.

Deep machine learning provides state-of-the-art performance in image-based plant phenotyping.

Pound MP, Atkinson JA, Townsend AJ, Wilson MH, Griffiths M, Jackson AS, Bulat A, Tzimiropoulos G, Wells DM, Murchie EH, Pridmore TP, French AP.

Gigascience. 2017 Oct 1;6(10):1-10. doi: 10.1093/gigascience/gix083. Erratum in: Gigascience. 2018 Jul 1;7(7):.

9.

Plant Phenomics, From Sensors to Knowledge.

Tardieu F, Cabrera-Bosquet L, Pridmore T, Bennett M.

Curr Biol. 2017 Aug 7;27(15):R770-R783. doi: 10.1016/j.cub.2017.05.055. Review.

10.

Quantification of root water uptake in soil using X-ray computed tomography and image-based modelling.

Daly KR, Tracy SR, Crout NMJ, Mairhofer S, Pridmore TP, Mooney SJ, Roose T.

Plant Cell Environ. 2018 Jan;41(1):121-133. doi: 10.1111/pce.12983. Epub 2017 Jul 5.

PMID:
28503782
11.

Root hydrotropism is controlled via a cortex-specific growth mechanism.

Dietrich D, Pang L, Kobayashi A, Fozard JA, Boudolf V, Bhosale R, Antoni R, Nguyen T, Hiratsuka S, Fujii N, Miyazawa Y, Bae TW, Wells DM, Owen MR, Band LR, Dyson RJ, Jensen OE, King JR, Tracy SR, Sturrock CJ, Mooney SJ, Roberts JA, Bhalerao RP, Dinneny JR, Rodriguez PL, Nagatani A, Hosokawa Y, Baskin TI, Pridmore TP, De Veylder L, Takahashi H, Bennett MJ.

Nat Plants. 2017 May 8;3:17057. doi: 10.1038/nplants.2017.57.

PMID:
28481327
12.

SuRVoS: Super-Region Volume Segmentation workbench.

Luengo I, Darrow MC, Spink MC, Sun Y, Dai W, He CY, Chiu W, Pridmore T, Ashton AW, Duke EMH, Basham M, French AP.

J Struct Biol. 2017 Apr;198(1):43-53. doi: 10.1016/j.jsb.2017.02.007. Epub 2017 Feb 27.

13.

The 4-Dimensional Plant: Effects of Wind-Induced Canopy Movement on Light Fluctuations and Photosynthesis.

Burgess AJ, Retkute R, Preston SP, Jensen OE, Pound MP, Pridmore TP, Murchie EH.

Front Plant Sci. 2016 Sep 21;7:1392. eCollection 2016.

14.

Extracting multiple interacting root systems using X-ray microcomputed tomography.

Mairhofer S, Sturrock CJ, Bennett MJ, Mooney SJ, Pridmore TP.

Plant J. 2015 Dec;84(5):1034-43. doi: 10.1111/tpj.13047.

15.

High-Resolution Three-Dimensional Structural Data Quantify the Impact of Photoinhibition on Long-Term Carbon Gain in Wheat Canopies in the Field.

Burgess AJ, Retkute R, Pound MP, Foulkes J, Preston SP, Jensen OE, Pridmore TP, Murchie EH.

Plant Physiol. 2015 Oct;169(2):1192-204. doi: 10.1104/pp.15.00722. Epub 2015 Aug 17.

16.

Root system markup language: toward a unified root architecture description language.

Lobet G, Pound MP, Diener J, Pradal C, Draye X, Godin C, Javaux M, Leitner D, Meunier F, Nacry P, Pridmore TP, Schnepf A.

Plant Physiol. 2015 Mar;167(3):617-27. doi: 10.1104/pp.114.253625. Epub 2015 Jan 22.

17.

Automated recovery of three-dimensional models of plant shoots from multiple color images.

Pound MP, French AP, Murchie EH, Pridmore TP.

Plant Physiol. 2014 Dec;166(4):1688-98. doi: 10.1104/pp.114.248971. Epub 2014 Oct 20.

18.

Mechanical modelling quantifies the functional importance of outer tissue layers during root elongation and bending.

Dyson RJ, Vizcay-Barrena G, Band LR, Fernandes AN, French AP, Fozard JA, Hodgman TC, Kenobi K, Pridmore TP, Stout M, Wells DM, Wilson MH, Bennett MJ, Jensen OE.

New Phytol. 2014 Jun;202(4):1212-22. doi: 10.1111/nph.12764. Epub 2014 Mar 18.

19.

Systems analysis of auxin transport in the Arabidopsis root apex.

Band LR, Wells DM, Fozard JA, Ghetiu T, French AP, Pound MP, Wilson MH, Yu L, Li W, Hijazi HI, Oh J, Pearce SP, Perez-Amador MA, Yun J, Kramer E, Alonso JM, Godin C, Vernoux T, Hodgman TC, Pridmore TP, Swarup R, King JR, Bennett MJ.

Plant Cell. 2014 Mar;26(3):862-75. doi: 10.1105/tpc.113.119495. Epub 2014 Mar 14.

20.

Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots.

Muraro D, Mellor N, Pound MP, Help H, Lucas M, Chopard J, Byrne HM, Godin C, Hodgman TC, King JR, Pridmore TP, Helariutta Y, Bennett MJ, Bishopp A.

Proc Natl Acad Sci U S A. 2014 Jan 14;111(2):857-62. doi: 10.1073/pnas.1221766111. Epub 2013 Dec 31.

21.

Time-profiling fluorescent reporters in the Arabidopsis root.

Larrieu AP, French AP, Pridmore TP, Bennett MJ, Wells DM.

Methods Mol Biol. 2014;1056:11-7. doi: 10.1007/978-1-62703-592-7_2.

PMID:
24306858
22.

Sequential induction of auxin efflux and influx carriers regulates lateral root emergence.

Péret B, Middleton AM, French AP, Larrieu A, Bishopp A, Njo M, Wells DM, Porco S, Mellor N, Band LR, Casimiro I, Kleine-Vehn J, Vanneste S, Sairanen I, Mallet R, Sandberg G, Ljung K, Beeckman T, Benkova E, Friml J, Kramer E, King JR, De Smet I, Pridmore T, Owen M, Bennett MJ.

Mol Syst Biol. 2013 Oct 22;9:699. doi: 10.1038/msb.2013.43.

23.

Effects of X-Ray Dose On Rhizosphere Studies Using X-Ray Computed Tomography.

Zappala S, Helliwell JR, Tracy SR, Mairhofer S, Sturrock CJ, Pridmore T, Bennett M, Mooney SJ.

PLoS One. 2013 Jun 26;8(6):e67250. doi: 10.1371/journal.pone.0067250. Print 2013.

24.

RootNav: navigating images of complex root architectures.

Pound MP, French AP, Atkinson JA, Wells DM, Bennett MJ, Pridmore T.

Plant Physiol. 2013 Aug;162(4):1802-14. doi: 10.1104/pp.113.221531. Epub 2013 Jun 13.

25.

Recovering complete plant root system architectures from soil via X-ray μ-Computed Tomography.

Mairhofer S, Zappala S, Tracy S, Sturrock C, Bennett MJ, Mooney SJ, Pridmore TP.

Plant Methods. 2013 Mar 20;9(1):8. doi: 10.1186/1746-4811-9-8.

26.

Multiscale systems analysis of root growth and development: modeling beyond the network and cellular scales.

Band LR, Fozard JA, Godin C, Jensen OE, Pridmore T, Bennett MJ, King JR.

Plant Cell. 2012 Oct;24(10):3892-906. doi: 10.1105/tpc.112.101550. Epub 2012 Oct 30. Review.

27.

What lies beneath: underlying assumptions in bioimage analysis.

Pridmore TP, French AP, Pound MP.

Trends Plant Sci. 2012 Dec;17(12):688-92. doi: 10.1016/j.tplants.2012.07.003. Epub 2012 Aug 17. Review.

PMID:
22902890
28.

Semi-automated CCTV surveillance: the effects of system confidence, system accuracy and task complexity on operator vigilance, reliance and workload.

Dadashi N, Stedmon AW, Pridmore TP.

Appl Ergon. 2013 Sep;44(5):730-8. doi: 10.1016/j.apergo.2012.04.012. Epub 2012 Jun 13.

PMID:
22704458
29.

Recovering the dynamics of root growth and development using novel image acquisition and analysis methods.

Wells DM, French AP, Naeem A, Ishaq O, Traini R, Hijazi HI, Bennett MJ, Pridmore TP.

Philos Trans R Soc Lond B Biol Sci. 2012 Jun 5;367(1595):1517-24. doi: 10.1098/rstb.2011.0291. Erratum in: Philos Trans R Soc Lond B Biol Sci. 2012 Aug 5;367(1599):2245. Hijazi, Hussein [corrected to Hijazi, Hussein I].

30.

CellSeT: novel software to extract and analyze structured networks of plant cells from confocal images.

Pound MP, French AP, Wells DM, Bennett MJ, Pridmore TP.

Plant Cell. 2012 Apr;24(4):1353-61. doi: 10.1105/tpc.112.096289. Epub 2012 Apr 3.

31.

Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.

Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ.

Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):4668-73. doi: 10.1073/pnas.1201498109. Epub 2012 Mar 5.

32.

Identifying biological landmarks using a novel cell measuring image analysis tool: Cell-o-Tape.

French AP, Wilson MH, Kenobi K, Dietrich D, Voß U, Ubeda-Tomás S, Pridmore TP, Wells DM.

Plant Methods. 2012 Mar 2;8:7. doi: 10.1186/1746-4811-8-7.

33.

RooTrak: automated recovery of three-dimensional plant root architecture in soil from x-ray microcomputed tomography images using visual tracking.

Mairhofer S, Zappala S, Tracy SR, Sturrock C, Bennett M, Mooney SJ, Pridmore T.

Plant Physiol. 2012 Feb;158(2):561-9. doi: 10.1104/pp.111.186221. Epub 2011 Dec 21.

34.

High-throughput feature counting and measurement of roots.

Naeem A, French AP, Wells DM, Pridmore TP.

Bioinformatics. 2011 May 1;27(9):1337-8. doi: 10.1093/bioinformatics/btr126. Epub 2011 Mar 12.

PMID:
21398671
35.

Atlas-guided correction of brain histology distortion.

Qiu X, Shi L, Pridmore T, Pitiot A, Wang D.

J Pathol Inform. 2011;2:S7. doi: 10.4103/2153-3539.92038. Epub 2012 Jan 19.

36.

Short-Root regulates primary, lateral, and adventitious root development in Arabidopsis.

Lucas M, Swarup R, Paponov IA, Swarup K, Casimiro I, Lake D, Peret B, Zappala S, Mairhofer S, Whitworth M, Wang J, Ljung K, Marchant A, Sandberg G, Holdsworth MJ, Palme K, Pridmore T, Mooney S, Bennett MJ.

Plant Physiol. 2011 Jan;155(1):384-98. doi: 10.1104/pp.110.165126. Epub 2010 Oct 27.

37.

Smooth 3-D reconstruction for 2-D histological images.

Cifor A, Pridmore T, Pitiot A.

Inf Process Med Imaging. 2009;21:350-61.

PMID:
19694276
38.

High-throughput quantification of root growth using a novel image-analysis tool.

French A, Ubeda-Tomás S, Holman TJ, Bennett MJ, Pridmore T.

Plant Physiol. 2009 Aug;150(4):1784-95. doi: 10.1104/pp.109.140558. Epub 2009 Jun 10.

39.

Validation of a novel computer-assisted sperm analysis (CASA) system using multitarget-tracking algorithms.

Tomlinson MJ, Pooley K, Simpson T, Newton T, Hopkisson J, Jayaprakasan K, Jayaprakasan R, Naeem A, Pridmore T.

Fertil Steril. 2010 Apr;93(6):1911-20. doi: 10.1016/j.fertnstert.2008.12.064. Epub 2009 Feb 6.

PMID:
19200972
40.

Clinical evaluation of a non-immersive virtual environment in stroke rehabilitation.

Edmans J, Gladman J, Hilton D, Walker M, Sunderland A, Cobb S, Pridmore T, Thomas S.

Clin Rehabil. 2009 Feb;23(2):106-16. doi: 10.1177/0269215508095875.

PMID:
19164398
41.

Colocalization of fluorescent markers in confocal microscope images of plant cells.

French AP, Mills S, Swarup R, Bennett MJ, Pridmore TP.

Nat Protoc. 2008;3(4):619-28. doi: 10.1038/nprot.2008.31.

PMID:
18388944
42.

Validity of a virtual environment for stroke rehabilitation.

Edmans JA, Gladman JR, Cobb S, Sunderland A, Pridmore T, Hilton D, Walker MF.

Stroke. 2006 Nov;37(11):2770-5. Epub 2006 Sep 28.

PMID:
17008609

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