, Volume 247, Issue 5, pp 1163–1173 | Cite as

FlowerMorphology: fully automatic flower morphometry software

  • Sergey M. Rozov
  • Elena V. Deineko
  • Igor V. Deyneko
Original Article


Main conclusion

The software FlowerMorphology is designed for automatic morphometry of actinomorphic flowers. The novel complex parameters of flowers calculated by FlowerMorphology allowed us to quantitatively characterize a polyploid series of tobacco.

Morphological differences of plants representing closely related lineages or mutants are mostly quantitative. Very often, there are only very fine variations in plant morphology. Therefore, accurate and high-throughput methods are needed for their quantification. In addition, new characteristics are necessary for reliable detection of subtle changes in morphology. FlowerMorphology is an all-in-one software package to automatically image and analyze five-petal actinomorphic flowers of the dicotyledonous plants. Sixteen directly measured parameters and ten calculated complex parameters of a flower allow us to characterize variations with high accuracy. The program was developed for the needs of automatic characterization of Nicotiana tabacum flowers, but is applicable to many other plants with five-petal actinomorphic flowers and can be adopted for flowers of other merosity. A genetically similar polyploid series of N. tabacum plants was used to investigate differences in flower morphology. For the first time, we could quantify the dependence between ploidy and size and form of the tobacco flowers. We found that the radius of inner petal incisions shows a persistent positive correlation with the chromosome number. In contrast, a commonly used parameter—radius of outer corolla—does not discriminate 2n and 4n plants. Other parameters show that polyploidy leads to significant aberrations in flower symmetry and are also positively correlated with chromosome number. Executables of FlowerMorphology, source code, documentation, and examples are available at the program website:


Automatic image acquisition and analysis Flower morphology Flower shape Flower symmetry 



Center of a circle around external vertices


Center of a circle around internal vertices


Center of a circle around a corolla tube


Radius of a circle around external vertices


Radius of a circle around internal vertices


Radius of a circle around a corolla tube


Area of a corolla tube


Geometrical asymmetry of (petal) incisions



This work has been supported by the program of SB RAS № 0324-2018-0017. The authors are grateful to A. Zagorskaya, Y. Sidorchuk, and S. Mursalimov for providing the polyploid series of N. tabacum, to F. Pessler for editing the manuscript and to one of the reviewers for thorough proofreading and valuable suggestions.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Availability of data and material

Executables, source code, documentation, and examples are available at the program website:

Supplementary material

425_2018_2856_MOESM1_ESM.docx (195 kb)
Supplementary material 1 (DOCX 194 kb)


  1. Adams DC, Rohlf FJ, Slice DE (2004) Geometric morphometrics: ten years of progress following the revolution. Ital J Zool 71:5–16CrossRefGoogle Scholar
  2. Andrade IM, Mayo SJ, Kirkup D, Van Den Berg C (2008) Comparative morphology of populations of Monstera Adans. (Araceae) from natural forest fragments in Northeast Brazil using elliptic Fourier analysis of leaf outlines. Kew Bull 63:193–211CrossRefGoogle Scholar
  3. Bissel EK, Diggle PK (2010) Modular genetic architecture of floral morphology in Nicotiana: quantitative genetic and comparative phenotypic approaches to floral integration. J Evol Biol 23:1744–1758CrossRefGoogle Scholar
  4. Cardozo AP, Temponi LG, Andrade IM, Mayo SJ, Smidt EC (2014) A morphometric and taxonomic study of Anthurium augustinum complex (Araceae), endemic to the Brazilian Atlantic Forest. Feddes Repert 125:43–58CrossRefGoogle Scholar
  5. Chen CY, Butts CL, Dang PM, Wang ML (2015) Advances in phenotyping of functional traits. In: Kumar J, Pratap A, Kumar S (eds) Phenomics in crop plants: trends, options and limitations. Springer India, New Delhi, pp 163–180Google Scholar
  6. Deyneko IV, Kel AE, Bloecker H, Kauer G (2005) Signal-theoretical DNA similarity measure revealing unexpected similarities of E. coli promoters. In Silico Biol 5:547–555PubMedGoogle Scholar
  7. Deyneko IV, Bredohl B, Wesely D, Kalybaeva YM, Kel AE, Blocker H, Kauer G (2006) FeatureScan: revealing property-dependent similarity of nucleotide sequences. Nucleic Acids Res 34:W591–W595CrossRefPubMedPubMedCentralGoogle Scholar
  8. Gardner AG, Gerald JNF, Menz J, Shepherd KA, Howarth DG, Jabaily RS (2016) Characterizing floral symmetry in the Core Goodeniaceae with geometric morphometrics. PLoS ONE 11:e0154736. CrossRefPubMedPubMedCentralGoogle Scholar
  9. Genaev MA, Doroshkov AV, Pshenichnikova TA, Kolchanov NA, Afonnikov DA (2012) Extraction of quantitative characteristics describing wheat leaf pubescence with a novel image-processing technique. Planta 236:1943–1954. CrossRefPubMedGoogle Scholar
  10. Helsen P, Van Dongen S (2016) Associations between floral asymmetry and individual genetic variability differ among three prickly pear (Opuntia echios) populations. Symmetry 8:116. CrossRefGoogle Scholar
  11. Hsu HC, Chen CY, Lee TK, Weng LK, Yeh DM, Lin TT, Wang CN, Kuo YF (2015) Quantitative analysis of floral symmetry and tube dilation in an F2 cross of Sinningia speciosa. Sci Hortic 188:71–77CrossRefGoogle Scholar
  12. Hu MK (1962) Visual pattern recognition by moment invariants. IRE Trans Inf Theory 8:179–187Google Scholar
  13. Klingenberg CP (2011) MorphoJ: an integrated software package for geometric morphometrics. Mol Ecol Resour 11:353–357CrossRefPubMedGoogle Scholar
  14. Klingenberg CP (2015) Analyzing fluctuating asymmetry with geometric morphometrics: concepts, methods, and applications. Symmetry 7:843–934CrossRefGoogle Scholar
  15. Kloster M, Kauer G, Beszteri B (2014) SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects. BMC Bioinform 15:218. CrossRefGoogle Scholar
  16. Kuhl FP, Giardina CR (1982) Elliptic Fourier features of a closed contour. Comput Gr Image Proc 18:236–258CrossRefGoogle Scholar
  17. Linker R, Cohen O, Naor A (2012) Determination of the number of green apples in RGB images recorded in orchards. Comput Electron Agric 81:45–57CrossRefGoogle Scholar
  18. Maliga P, Sz.-Breznovits A, Márton L (1973) Streptomycin-resistant plants from callus culture of haploid tobacco. Nat New Biol 244(131):29–30CrossRefPubMedGoogle Scholar
  19. Mann DG, McDonald SM, Bayer MM, Droop SJM, Chepurnov VA, Loke RE, Ciobanu A, du Buf JMH (2004) The Sellaphora pupula species complex (Bacillariophyceae): morphometric analysis, ultrastructure and mating data provide evidence for five new species. Phycologia 43(4):459–482CrossRefGoogle Scholar
  20. Marks CE, Newbigin E, Ladiges PY (2011) Comparative morphology and phylogeny of Nicotiana section Suaveolentes (Solanaceae) in Australia and the South Pacific. Aust Syst Bot 24:61–86CrossRefGoogle Scholar
  21. Mursalimov S, Deineko E (2017) Cytomixis in tobacco microsporogenesis: are there any genome parts predisposed to migration? Protoplasma 254:1379–1384. CrossRefPubMedGoogle Scholar
  22. Mursalimov S, Sidorchuk Y, Demidov D, Meister A, Deineko E (2016) A rise of ploidy level influences the rate of cytomixis in tobacco male meiosis. Protoplasma 253:1583–1588. CrossRefPubMedGoogle Scholar
  23. Narkhede HP (2013) Review of image segmentation techniques. Int J Sci Mod Eng 1:54–61Google Scholar
  24. Parekh HS, Thakore DG, Jaliya UK (2014) A survey on object detection and tracking methods. Int J Innov Res Comput Commun Eng 2:2970–2979Google Scholar
  25. Radović S, Urošević A, Hočevar K, Vuleta A, Manitašević-Jovanović S, Tucić B (2017) Geometric morphometrics of functionally distinct floral organs in Iris pumila: analyzing patterns of symmetric and asymmetric shape variations. Arch Biol Sci 69:223–231CrossRefGoogle Scholar
  26. Rapp RA, Wendel JF (2005) Epigenetics and plant evolution. New Phytol 168:81–91. CrossRefPubMedGoogle Scholar
  27. Restif C, Ibanez-Ventoso C, Vora MM, Guo S, Metaxas D, Driscoll M (2014) CeleST: computer vision software for quantitative analysis of C. elegans swim behavior reveals novel features of locomotion. PLoS Comput Biol 10:e1003702. CrossRefPubMedPubMedCentralGoogle Scholar
  28. Russ JC (2016) The image processing handbook. CRC Press, Boca RatonGoogle Scholar
  29. Saxena L, Armstrong L (2014) A survey of image processing techniques for agriculture. Proc AFITA 2014:401–413Google Scholar
  30. Scassellati E, Lucchese F, Abbate G (2013) A morphometric study of Armeria canescens aggr. (Plumbaginaceae) in the Italian Peninsula. Plant Biosyst 147:743–750CrossRefGoogle Scholar
  31. Shukla SKCX, Cortese G, Nayak GN (2013) Climate mediated size variability of diatom Fragilariopsis kerguelensis in the Southern Ocean. Quat Sci Rev 69:49–58CrossRefGoogle Scholar
  32. Sidorchuk YV, Deineko EV (2014) Deformation of nuclei and abnormal spindles assembly in the second male meiosis of polyploid tobacco plants. Cell Biol Int 38:472–479. CrossRefPubMedGoogle Scholar
  33. Sidorchuk YV, Deineko EV, Shumny VK (2007) Role of microtubular cytoskeleton and callose walls in the manifestation of cytomixis in pollen mother cells of tobacco Nicotiana tabacum L. Cell Tissue Biol 1(6):577–581CrossRefGoogle Scholar
  34. Silva MFS, De Andrade IM, Mayo SJ (2012) Geometric morphometrics of leaf blade shape in Montrichardia linifera (Araceae) populations from the Rio Parnaíba Delta, north-east Brazil. Bot J Linn Soc 170:554–572CrossRefGoogle Scholar
  35. Sinjushin AA, Bagheri A, Maassoumi AA, Rahiminejad MR (2015) Terata of two legume species with radialized corolla: some correlations in floral symmetry. Plant Syst Evol 301:2387–2397CrossRefGoogle Scholar
  36. Song Y, Glasbey CA, Horgan GW, Polder G, Dieleman JA, Van der Heijden GWAM (2014) Automatic fruit recognition and counting from multiple images. Biosyst Eng 118:203–215CrossRefGoogle Scholar
  37. Sozzani R, Busch W, Spalding EP, Benfey PN (2014) Advanced imaging techniques for the study of plant growth and development. Trends Plant Sci 19:304–310CrossRefPubMedPubMedCentralGoogle Scholar
  38. Stitz M, Hartl M, Baldwin IT, Gaquerel E (2014) Jasmonoyl-l-isoleucine coordinates metabolic networks required for anthesis and floral attractant emission in wild tobacco (Nicotiana attenuata). Plant Cell 26:3964–3983CrossRefPubMedPubMedCentralGoogle Scholar
  39. Vamosi JC, Goring SJ, Kennedy BF, Mayberry RJ, Moray CM, Neame LA, Tunbridge ND, Elle E (2007) Pollination, floral display, and the ecological correlates of polyploidy. Functional ecosystems and communities. Glob Sci Books 1:1–9Google Scholar
  40. Wang CC, Hsu HC, Wang CN, Kuo YF (2015) Morphological integration between floral petals for Sinnigia Speciosa. In: 2015 ASABE annual international meeting. American Society of Agricultural and Biological Engineers, p 1Google Scholar
  41. Wendel J, Doyle J (2005) Polyploidy and evolution in plants. Plant diversity and evolution. Genotypic and phenotypic variation in higher plants. CAB International, WallingfordGoogle Scholar
  42. Zelditch ML, Swiderski DL, Sheets HD (2012) Geometric morphometrics for biologists: a primer. Academic Press, CambridgeGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Laboratory of Bioengineering of PlantsInstitute of Cytology and Genetics SD RASNovosibirskRussia
  2. 2.Tomsk State UniversityTomskRussia
  3. 3.Biomarkers in Infection and ImmunityHelmholtz Centre for Infection ResearchBrunswickGermany
  4. 4.Institute of Microbiology and Braunschweig Integrated Center of Systems Biology (BRICS)Technische Universität BraunschweigBrunswickGermany

Personalised recommendations