An automatic segmentation method for scanned images of wheat root systems with dark discolourations

Jarosław Gocławski; Joanna Sekulska-Nalewajko; Ewa Gajewska; Marzena Wielanek

International Journal of Applied Mathematics and Computer Science (2009)

  • Volume: 19, Issue: 4, page 679-689
  • ISSN: 1641-876X

Abstract

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The analysis of plant root system images plays an important role in the diagnosis of plant health state, the detection of possible diseases and growth distortions. This paper describes an initial stage of automatic analysis-the segmentation method for scanned images of Ni-treated wheat roots from hydroponic culture. The main roots of a wheat fibrous system are placed separately in the scanner view area on a high chroma background (blue or red). The first stage of the method includes the transformation of a scanned RGB image into the HCI (Hue-Chroma-Intensity) colour space and then local thresholding of the chroma component to extract a binary root image. Possible chromatic discolourations, different from background colour, are added to the roots from blue or red chroma subcomponent images after thresholding. At the second stage, dark discolourations are extracted by local fuzzy c-means clustering of an HCI intensity image within the binary root mask. Fuzzy clustering is applied in local windows around the series of sample points on roots medial axes (skeleton). The performance of the proposed method is compared with hand-labelled segmentation for a series of several root systems.

How to cite

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Jarosław Gocławski, et al. "An automatic segmentation method for scanned images of wheat root systems with dark discolourations." International Journal of Applied Mathematics and Computer Science 19.4 (2009): 679-689. <http://eudml.org/doc/207966>.

@article{JarosławGocławski2009,
abstract = {The analysis of plant root system images plays an important role in the diagnosis of plant health state, the detection of possible diseases and growth distortions. This paper describes an initial stage of automatic analysis-the segmentation method for scanned images of Ni-treated wheat roots from hydroponic culture. The main roots of a wheat fibrous system are placed separately in the scanner view area on a high chroma background (blue or red). The first stage of the method includes the transformation of a scanned RGB image into the HCI (Hue-Chroma-Intensity) colour space and then local thresholding of the chroma component to extract a binary root image. Possible chromatic discolourations, different from background colour, are added to the roots from blue or red chroma subcomponent images after thresholding. At the second stage, dark discolourations are extracted by local fuzzy c-means clustering of an HCI intensity image within the binary root mask. Fuzzy clustering is applied in local windows around the series of sample points on roots medial axes (skeleton). The performance of the proposed method is compared with hand-labelled segmentation for a series of several root systems.},
author = {Jarosław Gocławski, Joanna Sekulska-Nalewajko, Ewa Gajewska, Marzena Wielanek},
journal = {International Journal of Applied Mathematics and Computer Science},
keywords = {root system image; segmentation; skeleton; root discolourations; fuzzy c-means clustering; root system; image segmentation},
language = {eng},
number = {4},
pages = {679-689},
title = {An automatic segmentation method for scanned images of wheat root systems with dark discolourations},
url = {http://eudml.org/doc/207966},
volume = {19},
year = {2009},
}

TY - JOUR
AU - Jarosław Gocławski
AU - Joanna Sekulska-Nalewajko
AU - Ewa Gajewska
AU - Marzena Wielanek
TI - An automatic segmentation method for scanned images of wheat root systems with dark discolourations
JO - International Journal of Applied Mathematics and Computer Science
PY - 2009
VL - 19
IS - 4
SP - 679
EP - 689
AB - The analysis of plant root system images plays an important role in the diagnosis of plant health state, the detection of possible diseases and growth distortions. This paper describes an initial stage of automatic analysis-the segmentation method for scanned images of Ni-treated wheat roots from hydroponic culture. The main roots of a wheat fibrous system are placed separately in the scanner view area on a high chroma background (blue or red). The first stage of the method includes the transformation of a scanned RGB image into the HCI (Hue-Chroma-Intensity) colour space and then local thresholding of the chroma component to extract a binary root image. Possible chromatic discolourations, different from background colour, are added to the roots from blue or red chroma subcomponent images after thresholding. At the second stage, dark discolourations are extracted by local fuzzy c-means clustering of an HCI intensity image within the binary root mask. Fuzzy clustering is applied in local windows around the series of sample points on roots medial axes (skeleton). The performance of the proposed method is compared with hand-labelled segmentation for a series of several root systems.
LA - eng
KW - root system image; segmentation; skeleton; root discolourations; fuzzy c-means clustering; root system; image segmentation
UR - http://eudml.org/doc/207966
ER -

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