Plant Image Analysis Plant Image Analysis

Complete bibliography


1.
ARIA
root-systemAnalysis of Maize (Zea mays L.) Seedling Roots with the High-Throughput Image Analysis Tool ARIA (Automatic Root Image Analysis).
J. Pace, N. Lee, HS. Naik, B. Ganapathysubramanian, T. Lübberstedt,
2014 , PLoS ONE , 9(9), 0

2.
ARTT
single-rootA novel tracking tool for the analysis of plant-root tip movements.
A. Russino, A. Ascrizzi, L. Popova, A. Tonazzini, S. Mancuso, B. Mazzolai,
2013 , Bioinspir Biomim , 8(2), 25004

3.
Balloon Plugin
cellIntegrated genetic and computation methods for in planta cytometry.
F. Federici, L. Dupuy, L. Laplaze, M. Heisler, J. Haseloff,
2012 , Nat. Methods , 9(5), 483

4.
BioImageXD
generalBioImageXD: an open, general-purpose and high-throughput image-processing platform.
P. Kankaanpää, L. Paavolainen, S. Tiitta, M. Karjalainen, J. Päivärinne, J. Nieminen, V. Marjomäki, J. Heino, DJ. White,
2012 , Nat. Methods , 9(7), 683

5.
BioLeaf
leafBioLeaf: A professional mobile application to measure foliar damage caused by insect herbivory
Bruno Brandoli Machadoa, Jonatan P M Oruea, Mauro S Arrudaa, Cleidimar V Santosa, Diogo S Sarathc, Wesley N Goncalvesa, Gercina G Silvac, Hemerson Pistoric, Antonia Railda Roelc
2016 , Computer and Eletronics in Agriculture , 129(1), 45

6.
Bisque
generalBisque: a platform for bioimage analysis and management.
K. Kvilekval, D. Fedorov, B. Obara, A. Singh, BS. Manjunath,
2010 , Bioinformatics , 26(4), 544

7.
Black Spot
leaf

Black Spot: a platform for automated and rapid estimation of leaf area from scanned images
Varma V. and Osuri A M
2013, Plant Ecol, 1-5

8.
BRAT
single-rootA Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis.
R. Slovak, C. Göschl, X. Su, K. Shimotani, T. Shiina, W. Busch,
2014 , Plant Cell , 0(0), 0

9.
Callose Measurer
cellCalloseMeasurer: a novel software solution to measure callose deposition and recognise spreading callose patterns.
J. Zhou, T. Spallek, C. Faulkner, S. Robatzek,
2012 , Plant Methods , 8(1), 49

10.
Canopy Analysis
canopy

Automated Analysis of in Situ Canopy Images for the Estimation of Forest Canopy Cover
Korhonen, L and Heikkinen, J
2009 Forest Science, Volume 55 (4),323-334

11.
Canopy Reconstruction
shootAutomated recovery of 3D models of plant shoots from multiple colour images.
MP. Pound, AP. French, EH. Murchie, TP. Pridmore,
2014 , Plant Physiol. , 0(0), 0

12.
Cefiler
cell

Automatic characterization of the cell organization in light microscopic images of wood: Application to the identification of the cell file
Brunel, Guilhem; Borianne, Philippe; Subsol, Gerard; Jaeger, Marc; Caraglio, Yves
Plant Growth Modeling, Simulation, Visualization and Applications (PMA), 2012 IEEE Fourth International Symposium on ,pp.58,65

13.
Cell-o-Tape
single-rootIdentifying biological landmarks using a novel cell measuring image analysis tool: Cell-o-Tape.
AP. French, MH. Wilson, K. Kenobi, D. Dietrich, U. Voß, S. Ubeda-Tomás, TP. Pridmore, DM. Wells,
2012 , Plant Methods , 8(0), 7

14.
CellProfiler
cellCellProfiler: image analysis software for identifying and quantifying cell phenotypes.
AE. Carpenter, TR. Jones, MR. Lamprecht, C. Clarke, IH. Kang, O. Friman, DA. Guertin, JH. Chang, RA. Lindquist, J. Moffat, P. Golland, DM. Sabatini,
2006 , Genome Biol. , 7(10), 0

15.
CellSeT
single-rootCellSeT: novel software to extract and analyze structured networks of plant cells from confocal images.
MP. Pound, AP. French, DM. Wells, MJ. Bennett, TP. Pridmore,
2012 , Plant Cell , 24(4), 1353

16.
Circumnutation Tracker
hypocotyl,shoot

Circumnutation Tracker: novel software for investigation of circumnutation
Maria Stolarz, Maciej Żuk, Elżbieta Król and Halina Dziubińska
Plant Methods 2014, 10:24

17.
CompuEye
leaf

A new software for measuring leaf area, and area damaged by Tetranychus urticae Koch.
Bakr, E. M.
2005 Journal of Applied Entomology 129 (3), 173-175.

18.
Cytomine
generalCollaborative analysis of multi-gigapixel imaging data using Cytomine.
R. Marée, L. Rollus, B. Stévens, R. Hoyoux, G. Louppe, R. Vandaele, JM. Begon, P. Kainz, P. Geurts, L. Wehenkel,
2016 , Bioinformatics , 0(0), 0

19.
DART
root-system

archiDART, an R package for the automated 2D computation of plant root architectural traits -
Delory B, Baudson C, Brostaux Y, Lobet G, du Jardin P, Pagès L and Delaplace P
2016, Plant and Soil, 398, 351-365
View at publisher



DART: a software to analyse root system architecture and development from captured images
Le Bot, J. et al.
2010, Plant and Soil, 326(1-2), pp.261–273.

20.
DIRT
root-systemImage-based high-throughput field phenotyping of crop roots.
A. Bucksch, J. Burridge, LM. York, A. Das, E. Nord, JS. Weitz, JP. Lynch,
2014 , Plant Physiol. , 0(0), 0

21.
DRACO-STEM
cell

**DRACO-STEM : an automatic tool to generate high-quality 3D meshes of meristem tissue at cell resolution. **
Cerutti, G., Ali, O., and Godin, C. (2017).
Front. Plant Sci. 8.

22.
DynamicRoots
root-systemDynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.
O. Symonova, CN. Topp, H. Edelsbrunner,
2015 , PLoS ONE , 10(6), 0

23.
Easy Leaf Area
leaf

Easy Leaf Area: Automated Digital Image Analysis for Rapid and Accurate Measurement of Leaf Area
Hsien Ming Easlon and Arnold J. Bloom
Applications in Plant Sciences, 2(7) 2014.

24.
ElonSim
root-system,simulation

Simulation of image acquisition in machine vision dedicated to seedling
elongation to validate image processing root segmentation algorithms

Landry Benoit, David Rousseau, Étienne Belin, Didier Demilly, François Chapeau-Blondeau
2014, Computers and Electronics in Agriculture, 114, 84-92

25.
Endomembrane Quantifier
cellSpatio-temporal cellular dynamics of the Arabidopsis flagellin receptor reveal activation status-dependent endosomal sorting.
M. Beck, J. Zhou, C. Faulkner, D. MacLean, S. Robatzek,
2012 , Plant Cell , 24(10), 4205

High-throughput confocal imaging of intact live tissue enables quantification of membrane trafficking in Arabidopsis.
S. Salomon, D. Grunewald, K. Stüber, S. Schaaf, D. MacLean, P. Schulze-Lefert, S. Robatzek,
2010 , Plant Physiol. , 154(3), 1096

26.
Endrov
generalEndrov: an integrated platform for image analysis.
J. Henriksson, J. Hench, YG. Tong, A. Johansson, D. Johansson, TR. Bürglin,
2013 , Nat. Methods , 10(6), 454

27.
EZ-Rhizo
root-systemEZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture.
P. Armengaud, K. Zambaux, A. Hills, R. Sulpice, RJ. Pattison, MR. Blatt, A. Amtmann,
2009 , Plant J. , 57(5), 945

EZ-Rhizo software: the gateway to root architecture analysis.
P. Armengaud,
2009 , Plant Signal Behav , 4(2), 139

28.
FibrilTool
cellFibrilTool, an ImageJ plug-in to quantify fibrillar structures in raw microscopy images.
A. Boudaoud, A. Burian, D. Borowska-Wykr?t, M. Uyttewaal, R. Wrzalik, D. Kwiatkowska, O. Hamant,
2014 , Nat Protoc , 9(2), 457

29.
Germinator
seedGERMINATOR: a software package for high-throughput scoring and curve fitting of Arabidopsis seed germination.
RV. Joosen, J. Kodde, LA. Willems, W. Ligterink, LH. van der Plas, HW. Hilhorst,
2010 , Plant J. , 62(1), 148

30.
GiA Roots
root-systemGiA Roots: software for the high throughput analysis of plant root system architecture.
T. Galkovskyi, Y. Mileyko, A. Bucksch, B. Moore, O. Symonova, CA. Price, CN. Topp, AS. Iyer-Pascuzzi, PR. Zurek, S. Fang, J. Harer, PN. Benfey, JS. Weitz,
2012 , BMC Plant Biol. , 12(0), 116

31.
GLO-RIA
root-systemGLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems.
R. Rellán-Álvarez, G. Lobet, H. Lindner, PL. Pradier, J. Sebastian, MC. Yee, Y. Geng, C. Trontin, T. LaRue, A. Schrager-Lavelle, CH. Haney, R. Nieu, J. Maloof, JP. Vogel, JR. Dinneny,
2015 , Elife , 4(0), 0

32.
GrainScan
seed

GrainScan: a low cost, fast method for grain size and colour measurements
Alex P Whan, Alison B Smith, Colin R Cavanagh, Jean P Ral, Lindsay M Shaw, Crispin A Howitt and Leanne Bischof
Plant Methods (2014) 10:23

33.
GrowScreen
rosetteDynamics of seedling growth acclimation towards altered light conditions can be quantified via GROWSCREEN: a setup and procedure designed for rapid optical phenotyping of different plant species.
A. Walter, H. Scharr, F. Gilmer, R. Zierer, KA. Nagel, M. Ernst, A. Wiese, O. Virnich, MM. Christ, B. Uhlig, S. Jünger, U. Schurr,
2007 , New Phytol. , 174(2), 447

34.
GrowScreen-Fluoro
shoot

Simultaneous phenotyping of leaf growth and chlorophyll fluorescence via GROWSCREEN FLUORO allows detection of stress tolerance in Arabidopsis thaliana and other rosette plants
Jansen, M., Gilmer, F., Biskup, B., Nagel, K. A., Rascher, U., Fischbach, A., Briem, S., Dreissen, G., Tittmann, S., Braun, S., De Jaeger, I.*, Metzlaff, M.*, Schurr, U., Scharr, H., Walter, A.
2009, Functional Plant Biology, 36(11), 902 - 914

35.
GrowScreen-Root
root-system

Temperature responses of roots: impact on growth, root system architecture and implications for phenotyping.
Kerstin A Nagel, Bernd Kastenholz, Siegfried Jahnke, Dagmar van Dusschoten, Til Aach, Matthias Mühlich, Daniel Truhn, Hanno Scharr, Stefan Terjung, Achim Walter, and Ulrich Schurr
2009, Functional Plant Biology, 36(11), p.947.

36.
GROW Map-Leaf
leafDynamics of leaf and root growth: endogenous control versus environmental impact.
A. Walter, U. Schurr,
2005 , Ann. Bot. , 95(6), 891

37.
GROW Map-Root
single-rootSpatio-temporal dynamics of expansion growth in roots: automatic quantification of diurnal course and temperature response by digital image sequence processing.
A. Walter, H. Spies, S. Terjung, R. Küsters, N. Kirchgessner, U. Schurr,
2002 , J. Exp. Bot. , 53(369), 689

38.
Growth Explorer
root-system
39.
HPGA
rosetteFunctional approach to high-throughput plant growth analysis.
OL. Tessmer, Y. Jiao, JA. Cruz, DM. Kramer, J. Chen,
2013 , BMC Syst Biol , 7(0), 0

40.
HTPheno
shootHTPheno: an image analysis pipeline for high-throughput plant phenotyping.
A. Hartmann, T. Czauderna, R. Hoffmann, N. Stein, F. Schreiber,
2011 , BMC Bioinformatics , 12(0), 148

41.
HyDE
hypocotylAutomated analysis of hypocotyl growth dynamics during shade avoidance in Arabidopsis.
B. Cole, SA. Kay, J. Chory,
2011 , Plant J. , 65(6), 991

42.
HypoPhen
hypocotylNuclear phytochrome A signaling promotes phototropism in Arabidopsis.
C. Kami, M. Hersch, M. Trevisan, T. Genoud, A. Hiltbrunner, S. Bergmann, C. Fankhauser,
2012 , Plant Cell , 24(2), 566

43.
HYPOTrace
hypocotylHYPOTrace: image analysis software for measuring hypocotyl growth and shape demonstrated on Arabidopsis seedlings undergoing photomorphogenesis.
L. Wang, IV. Uilecan, AH. Assadi, CA. Kozmik, EP. Spalding,
2009 , Plant Physiol. , 149(4), 1632

44.
IAP
shootIAP: an open-source information system for high-throughput plant phenotyping.
C. Klukas, D. Chen, JM. Pape,
2014 , Plant Physiol. , 0(0), 0

45.
Identify
leaf,plant

Interactive plant identification based on social image data
Alexis Joly, Hervé Goëau, Pierre Bonnet, Vera Bakic, Julien Barbe,
Souheil Selmi, Itheri Yahiaoui, Jennifer Carré, Elise Mouysset, Jean-François
Molino, Nozha Boujemaa, Daniel Barthélémy
2013, Ecological Informatics

46.
IJ_Rhizo
root-system

IJ_Rhizo: an open-source software to measure scanned images of root samples
Alain Pierret & Santimaitree Gonkhamdee & Christophe Jourdan & Jean-Luc Maeght
2013 Plant Soil

47.
ImAGE
canopy,leaf

Image-assisted gap estimation, a simple method for measuring grapevine leaf canopy density.
Hill GN, Beresford RM, Wood PN, Kim KS, Wright PJ (2011). Crop Science 51(6): 2801-2808.

48.
ImageJ
generalNIH Image to ImageJ: 25 years of image analysis.
CA. Schneider, WS. Rasband, KW. Eliceiri,
2012 , Nat. Methods , 9(7), 671

49.
img2net
generalimg2net: Automated network-based analysis of imaged phenotypes.
D. Breuer, Z. Nikoloski,
2014 , Bioinformatics , 0(0), 0

50.
iRoCS Toolbox
single-root,cellThe iRoCS Toolbox - 3D Analysis of the Plant Root Apical Meristem at Cellular Resolution.
T. Schmidt, T. Pasternak, K. Liu, T. Blein, D. Aubry-Hivet, A. Dovzhenko, J. Duerr, W. Teale, FA. Ditengou, H. Burkhardt, O. Ronneberger, K. Palme,
2014 , Plant J. , 0(0), 0

51.
KineRoot
single-rootA novel image-analysis technique for kinematic study of growth and curvature.
P. Basu, A. Pal, JP. Lynch, KM. Brown,
2007 , Plant Physiol. , 145(2), 305

52.
LAMINA
leafLAMINA: a tool for rapid quantification of leaf size and shape parameters.
M. Bylesjö, V. Segura, RY. Soolanayakanahally, AM. Rae, J. Trygg, P. Gustafsson, S. Jansson, NR. Street,
2008 , BMC Plant Biol. , 8(0), 82

53.
Lamina2Shape
leaf

Lamina2Shape—an image process- ing tool for an explicit description of lamina shape tested on winter wheat (Triticum aestivumL.).
Dornbusch T, Andrieu B
2010, Computers and Electronics in Agriculture, 70:217–224

54.
LEAF-GUI
leafLeaf extraction and analysis framework graphical user interface: segmenting and analyzing the structure of leaf veins and areoles.
CA. Price, O. Symonova, Y. Mileyko, T. Hilley, JS. Weitz,
2011 , Plant Physiol. , 155(1), 236

55.
LeafAnalyser
leafLeafAnalyser: a computational method for rapid and large-scale analyses of leaf shape variation.
C. Weight, D. Parnham, R. Waites,
2008 , Plant J. , 53(3), 578

56.
Leaf Angle Distribution Toolbox
shoot

The leaf angle distribution of natural plant populations: assessing the canopy with a novel software tool
Mark Müller-Linow*, Francisco Pinto-Espinosa, Hanno Scharr and Uwe Rascher
Plant Methods, 2015, 11:11

57.
Leaf Doctor
leaf

Leaf Doctor: A New Portable Application for Quantifying Plant Disease Severity
Sarah Jane Pethybridge and Scot C. Nelson
Plant Disease 2015

58.
Leaf Color Segmentation
rosette

A segmentation procedure using colour features applied to images of Arabidopsis thaliana
Ruben Ispiryan, Igor Grigoriev, Wolfgang zu Castell, and Anton R Schäffner
2013, Functional Plant Biology

59.
Leaf Growth
leafComputational method for quantifying growth patterns at the adaxial leaf surface in three dimensions.
L. Remmler, AG. Rolland-Lagan,
2012 , Plant Physiol. , 159(1), 27

60.
LeafJ
leafLeafJ: an ImageJ plugin for semi-automated leaf shape measurement.
JN. Maloof, K. Nozue, MR. Mumbach, CM. Palmer,
2013 , J Vis Exp , 0(71), 0

61.
Leaf Processor
leafLEAFPROCESSOR: a new leaf phenotyping tool using contour bending energy and shape cluster analysis.
A. Backhaus, A. Kuwabara, M. Bauch, N. Monk, G. Sanguinetti, A. Fleming,
2010 , New Phytol. , 187(1), 251

62.
Leaf recognition
leaf

Leaf recognition of woody species in Central Europe
Petr Novotny and Tomas Suk
2013, Biosystems engineering 115, 444-452

63.
LeafSnap
leaf

Leafsnap: A Computer Vision System for Automatic Plant Species Identification
Neeraj Kumar, Peter N. Belhumeur, Arijit Biswas, David W. Jacobs, W. John Kress, Ida C. Lopez and Joao V.B. Soares
2012 Computer Vision – ECCV 2012, Lecture Notes in Computer Science, pp 502-516

64.
Leaf Venation
leafQuantifying leaf venation patterns: two-dimensional maps.
AG. Rolland-Lagan, M. Amin, M. Pakulska,
2009 , Plant J. , 57(1), 195

65.
Leaver
leaf

Automated valuation of leaves area for large-scale analysis needing data coupling or petioles deletion Borianne, P.; Brunel, G.
2012 Plant Growth Modeling, Simulation, Visualization and Applications (PMA), IEEE Fourth International Symposium on, pp.50-57

66.
Limani
leafQuantitative analysis of venation patterns of Arabidopsis leaves by supervised image analysis.
S. Dhondt, D. Van Haerenborgh, C. Van Cauwenbergh, RM. Merks, W. Philips, GT. Beemster, D. Inzé,
2012 , Plant J. , 69(3), 553

67.
LithoGraphX
anyMorphoGraphX: A platform for quantifying morphogenesis in 4D.
P. Barbier de Reuille, AL. Routier-Kierzkowska, D. Kierzkowski, GW. Bassel, T. Schüpbach, G. Tauriello, N. Bajpai, S. Strauss, A. Weber, A. Kiss, A. Burian, H. Hofhuis, A. Sapala, M. Lipowczan, MB. Heimlicher, S. Robinson, EM. Bayer, K. Basler, P. Koumoutsakos, AH. Roeder, T. Aegerter-Wilmsen, N. Nakayama, M. Tsiantis, A. Hay, D. Kwiatkowska, I. Xenarios, C. Kuhlemeier, RS. Smith,
0 , Elife , 4(0), 0

68.
LobeFinder
cell,leafLobeFinder: a convex hull-based method for quantitative boundary analyses of lobed plant cells.
TC. Wu, S. Belteton, J. Pack, DB. Szymanski, D. Umulis,
2016 , Plant Physiol. , 0(0), 0

69.
MARS-ALT
cellImaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution.
R. Fernandez, P. Das, V. Mirabet, E. Moscardi, J. Traas, JL. Verdeil, G. Malandain, C. Godin,
2010 , Nat. Methods , 7(7), 547

70.
Martrack Leaf
leafDiel leaf growth of soybean: a novel method to analyze two-dimensional leaf expansion in high temporal resolution based on a marker tracking approach (Martrack Leaf).
M. Mielewczik, M. Friedli, N. Kirchgessner, A. Walter,
2013 , Plant Methods , 9(1), 30

71.
MicroFilament Analyser
cellMicroFilament Analyzer, an image analysis tool for quantifying fibrillar orientation, reveals changes in microtubule organization during gravitropism.
E. Jacques, J. Buytaert, DM. Wells, M. Lewandowski, MJ. Bennett, J. Dirckx, JP. Verbelen, K. Vissenberg,
2013 , Plant J. , 74(6), 1045

72.
MorphoGraphX
generalMorphoGraphX: A platform for quantifying morphogenesis in 4D.
P. Barbier de Reuille, AL. Routier-Kierzkowska, D. Kierzkowski, GW. Bassel, T. Schüpbach, G. Tauriello, N. Bajpai, S. Strauss, A. Weber, A. Kiss, A. Burian, H. Hofhuis, A. Sapala, M. Lipowczan, MB. Heimlicher, S. Robinson, EM. Bayer, K. Basler, P. Koumoutsakos, AH. Roeder, T. Aegerter-Wilmsen, N. Nakayama, M. Tsiantis, A. Hay, D. Kwiatkowska, I. Xenarios, C. Kuhlemeier, RS. Smith,
0 , Elife , 4(0), 0

73.
MorphoLeaf
leaf

Multiscale quantification of morphodynamics: MorphoLeaf, software for 2-D shape analysis

Eric Biot, Millán Cortizo, Jasmine Burguet, Annamaria Kiss, Mohammed Oughou, Aude Maugarny-Calès, Beatriz Gonçalves, Bernard Adroher, Philippe Andrey, Arezki Boudaoud, Patrick Laufs
Development 2016

74.
NMRooting
root-system

Quantitative 3D Analysis of Plant Roots growing in Soil using Magnetic Resonance Imaging
Dagmar van Dusschoten, Ralf Metzner, Johannes Kochs, Johannes A. Postma, Daniel Pflugfelder, Jonas Buehler, Ulrich Schurr and Siegfried Jahnke
Plant Physiology 2016

75.
OMERO
generalOMERO: flexible, model-driven data management for experimental biology.
C. Allan, JM. Burel, J. Moore, C. Blackburn, M. Linkert, S. Loynton, D. Macdonald, WJ. Moore, C. Neves, A. Patterson, M. Porter, A. Tarkowska, B. Loranger, J. Avondo, I. Lagerstedt, L. Lianas, S. Leo, K. Hands, RT. Hay, A. Patwardhan, C. Best, GJ. Kleywegt, G. Zanetti, JR. Swedlow,
2012 , Nat. Methods , 9(3), 245

76.
OSCILLATOR
rosetteOSCILLATOR: A system for analysis of diurnal leaf growth using infrared photography combined with wavelet transformation.
R. Bours, M. Muthuraman, H. Bouwmeester, A. van der Krol,
2012 , Plant Methods , 8(1), 29

77.
PANorama
fruitHigh-Resolution Inflorescence Phenotyping Using a Novel Image Analysis Pipeline, PANorama.
S. Crowell, AX. Falcão, A. Shah, Z. Wilson, AJ. Greenberg, SR. McCouch,
2014 , Plant Physiol. , 0(0), 0

78.
PhenoPhyte
leaf,rosettePhenoPhyte: a flexible affordable method to quantify 2D phenotypes from imagery.
JM. Green, H. Appel, EM. Rehrig, J. Harnsomburana, JF. Chang, P. Balint-Kurti, CR. Shyu,
2012 , Plant Methods , 8(1), 45

79.
Phenotic
leafHigh throughput quantitative phenotyping of plant resistance using chlorophyll fluorescence image analysis.
C. Rousseau, E. Belin, E. Bove, D. Rousseau, F. Fabre, R. Berruyer, J. Guillaumès, C. Manceau, MA. Jacques, T. Boureau,
2013 , Plant Methods , 9(1), 17

80.
phenoVein
leafphenoVein - A tool for leaf vein segmentation and analysis.
J. Bühler, L. Rishmawi, D. Pflugfelder, G. Huber, H. Scharr, M. Hülskamp, M. Koornneef, U. Schurr, S. Jahnke,
2015 , Plant Physiol. , 0(0), 0

81.
Phytotyping4D
rosette,leaf

Phytotyping4D: A light-field imaging system for non-invasive and accurate monitoring of spatiotemporal
plant growth

Federico Apelt, David Breuer, Zoran Nikoloski, Mark Stitt and Friedrich Kragler1
2015, The Plant Journal

82.
PHIV-RootCell
single-root

PHIV-RootCell: a supervised image analysis tool for rice root anatomical parameter quantification
Lartaud Marc, Perin Christophe, Courtois Brigitte, Thomas Emilie, Henry Sophia, Bettembourg Mathilde, Divol Fanchon, Lanau Nadege, Artus Florence, Bureau Charlotte, Verdeil Jean-Luc, Sarah Gautier, Guiderdoni Emmanuel, Dievart Anne
2014, Frontiers in Plant Sciences, 5

83.
PDQuant
leaf,cellA developmental framework for complex plasmodesmata formation revealed by large-scale imaging of the Arabidopsis leaf epidermis.
J. Fitzgibbon, M. Beck, J. Zhou, C. Faulkner, S. Robatzek, K. Oparka,
2013 , Plant Cell , 25(1), 57

84.
PlantCV
shoot,seed,rosette,leafLights, camera, action: high-throughput plant phenotyping is ready for a close-up.
N. Fahlgren, MA. Gehan, I. Baxter,
2015 , Curr. Opin. Plant Biol. , 24(0), 93

85.
PlantVis
single-root

Estimating the motion of plant root cells from in vivo confocal laser scanning microscopy images
Timothy J. Roberts, Stephen J. McKenna, Cheng-Jin Du, Nathalie Wuyts, Tracy A. Valentine, A. Glyn Bengough
2010, Machine Vision and Applications, 21:921–939

86.
P-Trap
fruitP-TRAP: a Panicle Trait Phenotyping Tool.
FM. Al-Tam, H. Adam, AD. Anjos, M. Lorieux, P. Larmande, A. Ghesquière, S. Jouannic, HR. Shahbazkia,
2013 , BMC Plant Biol. , 13(1), 122

87.
REST
root-system

Next generation shovelomics: set up a tent and REST
Tino Colombi, Norbert Kirchgessner, Chantal Andrée Le Marié, Larry Matthew York, Jonathan P. Lynch, Andreas Hund
Plant and Soil, 2015

88.
RhizoScan
root-system

An automated image-processing pipelinefor high-throughput analysis of root architecture in OpenAlea
J. Diener, P. Nacry, C. Périn, A. Dievart, X. Draye, F. Boudon, A. Gaujon, and C. Godin,
Presented at the FSPM13, 2013, 1–3.
View publications

89.
RNQS
root-systemStandardized mapping of nodulation patterns in legume roots.
L. Remmler, L. Clairmont, AG. Rolland-Lagan, FC. Guinel,
2014 , New Phytol. , 202(3), 1083

90.
RootAnalyzer
single-rootRootAnalyzer: A Cross-Section Image Analysis Tool for Automated Characterization of Root Cells and Tissues.
J. Chopin, H. Laga, CY. Huang, S. Heuer, SJ. Miklavcic,
2015 , PLoS ONE , 10(9), 0

91.
RootFlowRT
single-rootA new algorithm for computational image analysis of deformable motion at high spatial and temporal resolution applied to root growth. Roughly uniform elongation in the meristem and also, after an abrupt acceleration, in the elongation zone.
CM. van der Weele, HS. Jiang, KK. Palaniappan, VB. Ivanov, K. Palaniappan, TI. Baskin,
2003 , Plant Physiol. , 132(3), 1138

92.
RootFly
root-systemAutomatic discrimination of fine roots in minirhizotron images.
G. Zeng, ST. Birchfield, CE. Wells,
2008 , New Phytol. , 177(2), 549

93.
RootGraph
root-systemRootGraph: a graphic optimization tool for automated image analysis of plant roots.
J. Cai, Z. Zeng, JN. Connor, CY. Huang, V. Melino, P. Kumar, SJ. Miklavcic,
2015 , J. Exp. Bot. , 0(0), 0

94.
RootLM
single-root

RootLM: a simple color image analysis program for length measurement of primary roots in Arabidopsis.
Qi X, Qi J, Wu Y
2007 Plant Root 1: 10-16.

95.
RootNav
root-systemRootNav: Navigating images of complex root architectures.
MP. Pound, AP. French, J. Atkinson, DM. Wells, MJ. Bennett, TP. Pridmore,
2013 , Plant Physiol. , 0(0), 0

96.
rosettR
rosette

rosettR: protocol and software for seedling area and growth analysis.
Tomé, F., Jansseune, K., Saey, B., Grundy, J., Vandenbroucke, K., Hannah, M.A., and Redestig, H.
Plant Methods 13: 13. 2017

97.
ROXAS
shoot

ROXAS – A new tool to build centuries-long tracheid-lumen chronologies in conifers
Georg von Arx, Marco Carrer
2014, Dendrochronologia

98.
RTipC
root-system

Root phenotyping by root tip detection and classification through statistical learning
Kumar, P. Huang, C. Cai, J. Miklavcic, S.J.,
Plant and Soil, 380, Issue 1-2 , pp 193-209, March 2014.

99.
RootTip Trace
single-rootA spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis.
Y. Geng, R. Wu, CW. Wee, F. Xie, X. Wei, PM. Chan, C. Tham, L. Duan, JR. Dinneny,
2013 , Plant Cell , 25(6), 2132

100.
RooTrak
root-systemRooTrak: automated recovery of three-dimensional plant root architecture in soil from x-ray microcomputed tomography images using visual tracking.
S. Mairhofer, S. Zappala, SR. Tracy, C. Sturrock, M. Bennett, SJ. Mooney, T. Pridmore,
2012 , Plant Physiol. , 158(2), 561

Recovering complete plant root system architectures from soil via X-ray ?-Computed Tomography.
S. Mairhofer, S. Zappala, S. Tracy, C. Sturrock, MJ. Bennett, SJ. Mooney, TP. Pridmore,
2013 , Plant Methods , 9(1), 8

101.
RootReader2D
root-system

High-throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development.
Clark R T, Famoso A N, Zhao K, Shaff J E, Craft E J, Bustamante C D, McCouch S R, Aneshansley D J, Kochian L V
2013, Plant Cell and Environment 36 (2), 454–466

102.
RootReader3D
root-system

3-Dimensional Root Phenotyping with a Novel Imaging and Software Platform.
R Clark, R MacCurdy, J Jung, J Shaff, S R McCouch, D Aneshansley, and L Kochian
2011, Plant Physiology, 156, 455-465.

103.
RootScan
single-root

RootScan: Software for high-throughput analysis of root anatomical traits
Burton, A.L. , M Williams, J P Lynch, and K M Brown
2012, Plant and Soil, 357(1-2), 189-203

104.
RootScape
root-systemRootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis.
D. Ristova, U. Rosas, G. Krouk, S. Ruffel, KD. Birnbaum, GM. Coruzzi,
2013 , Plant Physiol. , 161(3), 1086

105.
Root System Analyser
root-systemRecovering root system traits using image analysis - Exemplified by 2-dimensional neutron radiography images of lupine.
D. Leitner, B. Felderer, P. Vontobel, A. Schnepf,
2013 , Plant Physiol. , 0(0), 0

106.
RootTrace
root-system, single-rootHigh-throughput quantification of root growth using a novel image-analysis tool.
A. French, S. Ubeda-Tomás, TJ. Holman, MJ. Bennett, T. Pridmore,
2009 , Plant Physiol. , 150(4), 1784

High-throughput feature counting and measurement of roots.
A. Naeem, AP. French, DM. Wells, TP. Pridmore,
2011 , Bioinformatics , 27(9), 1337

107.
Rosette Tracker
rosetteRosette tracker: an open source image analysis tool for automatic quantification of genotype effects.
J. De Vylder, F. Vandenbussche, Y. Hu, W. Philips, D. Van Der Straeten,
2012 , Plant Physiol. , 160(3), 1149

108.
SeedSize
seedMapping quantitative trait loci affecting Arabidopsis thaliana seed morphology features extracted computationally from images.
CR. Moore, DS. Gronwall, ND. Miller, EP. Spalding,
2013 , G3 (Bethesda) , 3(1), 109

109.
SHAPE
generalSHAPE: a computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors.
H. Iwata, Y. Ukai,
0 , J. Hered. , 93(5), 384

110.
SmartGrain
seedSmartGrain: high-throughput phenotyping software for measuring seed shape through image analysis.
T. Tanabata, T. Shibaya, K. Hori, K. Ebana, M. Yano,
2012 , Plant Physiol. , 160(4), 1871

111.
SmartRoot
root-systemA novel image-analysis toolbox enabling quantitative analysis of root system architecture.
G. Lobet, L. Pagès, X. Draye,
2011 , Plant Physiol. , 157(1), 29

112.
Sorghum Reconstruction
shoot3D sorghum reconstructions from depth images identify QTL regulating shoot architecture.
RF. Mccormick, SK. Truong, JE. Mullet,
2016 , Plant Physiol. , 0(0), 0

113.
Stalk Analyzer
shoot

Image analysis of anatomical traits in stalk transections of maize and other grasses
Sven Heckwolf, Marlies Heckwolf, Shawn M Kaeppler, Natalia de Leon and Edgar P Spalding
2015, Plant Methods

114.
TIPS
flower

TIPS: a system for automated image-based phenotyping of maize tassels.
Gage, J.L., Miller, N.D., Spalding, E.P., Kaeppler, S.M., and de Leon, N. (2017).
Plant Methods 13: 21.

115.
Tomato Analyser
fruitDevelopment of a controlled vocabulary and software application to analyze fruit shape variation in tomato and other plant species.
MT. Brewer, L. Lang, K. Fujimura, N. Dujmovic, S. Gray, E. van der Knaap,
2006 , Plant Physiol. , 141(1), 15

116.
TraitMill
shoot

TraitmillTM: a functional genomics platform for the phenotypic analysis of cereals.
Reuzeau C, Frankard V, Hatzfeld Y, Sanz A, Van Camp W, Lejeune P, De Wilde C, Lievens K, de Wolf J, Vranken E
2006 Plant Gen Res 4:20

117.
TrichEratops
cellSemi-automated 3D leaf reconstruction and analysis of trichome patterning from light microscopic images.
H. Failmezger, B. Jaegle, A. Schrader, M. Hülskamp, A. Tresch,
2013 , PLoS Comput. Biol. , 9(4), 0

118.
TRiP
shoot

TRiP: Tracking Rhythms in Plants, an automated leaf movement analysis program for circadian period estimation
Kathleen Greenham, Ping Lou, Sara E Remsen, Hany Farid and Robertson McClung
Plant Methods 2015, 11:33

119.
Vaa3D
generalV3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets.
H. Peng, Z. Ruan, F. Long, JH. Simpson, EW. Myers,
2010 , Nat. Biotechnol. , 28(4), 348

Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model.
H. Peng, Z. Ruan, D. Atasoy, S. Sternson,
2010 , Bioinformatics , 26(12), 0

Extensible visualization and analysis for multidimensional images using Vaa3D.
H. Peng, A. Bria, Z. Zhou, G. Iannello, F. Long,
2014 , Nat Protoc , 9(1), 193

120.
VitiCanopy
canopyVitiCanopy: A Free Computer App to Estimate Canopy Vigor and Porosity for Grapevine.
R. De Bei, S. Fuentes, M. Gilliham, S. Tyerman, E. Edwards, N. Bianchini, J. Smith, C. Collins,
2016 , Sensors (Basel) , 16(4), 0

121.
WinRhizo
root-system

WinRHIZO™, a root-measuring system with a unique overlap correction method.
Arsenault, J.-L., S. Pouleur, C. Messier, and R. Guay
1995, HortScience 30: 906.

122.
Image Harvest
shootImage Harvest: an open-source platform for high-throughput plant image processing and analysis.
AC. Knecht, MT. Campbell, A. Caprez, DR. Swanson, H. Walia,
2016 , J. Exp. Bot. , 0(0), 0

123.
WinRhizoTRON
root-system

WinRHIZO™, a root-measuring system with a unique overlap correction method.
Arsenault, J.-L., S. Pouleur, C. Messier, and R. Guay
1995, HortScience 30: 906.

124.
Maize Kernel-Ear-Cob Analysis
fruitA robust, high-throughput method for computing maize ear, cob, and kernel attributes automatically from images.
ND. Miller, NJ. Haase, J. Lee, SM. Kaeppler, N. de Leon, EP. Spalding,
2016 , Plant J. , 0(0), 0

125.
AutoRoot
root-system

AutoRoot: open-source software employing a novel image analysis approach to support fully-automated plant phenotyping.
Pound, M.P., Fozard, S., Torres Torres, M., Forde, B.G., and French, A.P.
(2017). Plant Methods 13: 12.

126.
Leaf Shape Analysis
leafQuantifying shape changes and tissue deformation in leaf development.
AG. Rolland-Lagan, L. Remmler, C. Girard-Bock,
2014 , Plant Physiol. , 0(0), 0