SegOptim—A new R package for optimizing object-based image analyses of high-spatial resolution remotely-sensed data

João Gonçalves*, Isabel Pôças, Bruno Marcos, C.A. Mücher, João P. Honrado

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)

Abstract

Geographic Object-based Image Analysis (GEOBIA) is increasingly used to process high-spatial resolution imagery, with applications ranging from single species detection to habitat and land cover mapping. Image segmentation plays a key role in GEOBIA workflows, allowing to partition images into homogenous and mutually exclusive regions. Nonetheless, segmentation techniques require a robust parameterization to achieve the best results. Frequently, inappropriate parameterization leads to sub-optimal results and difficulties in comparing distinct methods. Here, we present an approach based on Genetic Algorithms (GA) to optimize image segmentation parameters by using the performance scores from object-based classification, thus allowing to assess the adequacy of a segmented image in relation to the classification problem. This approach was implemented in a new R package called SegOptim, in which several segmentation algorithms are interfaced, mostly from open-source software (GRASS GIS, Orfeo Toolbox, RSGISLib, SAGA GIS, TerraLib), but also from proprietary software (ESRI ArcGIS). SegOptim also provides access to several machine-learning classification algorithms currently available in R, including Gradient Boosted Modelling, Support Vector Machines, and Random Forest. We tested our approach using very-high to high spatial resolution images collected from an Unmanned Aerial Vehicle (0.03 – 0.10 m), WorldView-2 (2 m), RapidEye (5 m) and Sentinel-2 (10 – 20 m) in six different test sites located in northern Portugal with varying environmental conditions and for different purposes, including invasive species detection and land cover mapping. The results highlight the added value of our novel comparison of image segmentation and classification algorithms. Overall classification performances (assessed through cross-validation with the Kappa index) ranged from 0.85 to 1.00. Pilot-tests show that our GA-based approach is capable of providing sound results for optimizing the parameters of different segmentation algorithms, with benefits for classification accuracy and for comparison across techniques. We also verified that no particular combination of an image segmentation and a classification algorithm is suited for all the tasks/objectives. Consequently, it is crucial to compare and optimize available methods to understand which one is more suited for a certain objective. Our approach allows a closer integration between the segmentation and classification stages, which is of high importance for GEOBIA workflows. The results from our tests confirm that this integration has benefits for comparing and optimizing both processes. We discuss some limitations of the SegOptim approach (and potential solutions) as well as a future roadmap to expand its current functionalities.

Original languageEnglish
Pages (from-to)218-230
Number of pages13
JournalInternational Journal of applied Earth Observation and Geoinformation
Volume76
DOIs
Publication statusPublished - 1 Apr 2019

Fingerprint

segmentation
spatial resolution
Image segmentation
Image analysis
image analysis
Parameterization
Geographic information systems
genetic algorithm
Genetic algorithms
parameterization
land cover
GIS
software
Image classification
Image resolution
Unmanned aerial vehicles (UAV)
Support vector machines
Learning systems
invasive species
Acoustic waves

Keywords

  • Genetic algorithms
  • GEOBIA
  • Geographic object-based image analysis
  • High-spatial resolution
  • Image segmentation
  • Open-source software
  • Optimization
  • R package
  • Supervised classification

Cite this

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title = "SegOptim—A new R package for optimizing object-based image analyses of high-spatial resolution remotely-sensed data",
abstract = "Geographic Object-based Image Analysis (GEOBIA) is increasingly used to process high-spatial resolution imagery, with applications ranging from single species detection to habitat and land cover mapping. Image segmentation plays a key role in GEOBIA workflows, allowing to partition images into homogenous and mutually exclusive regions. Nonetheless, segmentation techniques require a robust parameterization to achieve the best results. Frequently, inappropriate parameterization leads to sub-optimal results and difficulties in comparing distinct methods. Here, we present an approach based on Genetic Algorithms (GA) to optimize image segmentation parameters by using the performance scores from object-based classification, thus allowing to assess the adequacy of a segmented image in relation to the classification problem. This approach was implemented in a new R package called SegOptim, in which several segmentation algorithms are interfaced, mostly from open-source software (GRASS GIS, Orfeo Toolbox, RSGISLib, SAGA GIS, TerraLib), but also from proprietary software (ESRI ArcGIS). SegOptim also provides access to several machine-learning classification algorithms currently available in R, including Gradient Boosted Modelling, Support Vector Machines, and Random Forest. We tested our approach using very-high to high spatial resolution images collected from an Unmanned Aerial Vehicle (0.03 – 0.10 m), WorldView-2 (2 m), RapidEye (5 m) and Sentinel-2 (10 – 20 m) in six different test sites located in northern Portugal with varying environmental conditions and for different purposes, including invasive species detection and land cover mapping. The results highlight the added value of our novel comparison of image segmentation and classification algorithms. Overall classification performances (assessed through cross-validation with the Kappa index) ranged from 0.85 to 1.00. Pilot-tests show that our GA-based approach is capable of providing sound results for optimizing the parameters of different segmentation algorithms, with benefits for classification accuracy and for comparison across techniques. We also verified that no particular combination of an image segmentation and a classification algorithm is suited for all the tasks/objectives. Consequently, it is crucial to compare and optimize available methods to understand which one is more suited for a certain objective. Our approach allows a closer integration between the segmentation and classification stages, which is of high importance for GEOBIA workflows. The results from our tests confirm that this integration has benefits for comparing and optimizing both processes. We discuss some limitations of the SegOptim approach (and potential solutions) as well as a future roadmap to expand its current functionalities.",
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year = "2019",
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SegOptim—A new R package for optimizing object-based image analyses of high-spatial resolution remotely-sensed data. / Gonçalves, João; Pôças, Isabel; Marcos, Bruno; Mücher, C.A.; Honrado, João P.

In: International Journal of applied Earth Observation and Geoinformation, Vol. 76, 01.04.2019, p. 218-230.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - SegOptim—A new R package for optimizing object-based image analyses of high-spatial resolution remotely-sensed data

AU - Gonçalves, João

AU - Pôças, Isabel

AU - Marcos, Bruno

AU - Mücher, C.A.

AU - Honrado, João P.

PY - 2019/4/1

Y1 - 2019/4/1

N2 - Geographic Object-based Image Analysis (GEOBIA) is increasingly used to process high-spatial resolution imagery, with applications ranging from single species detection to habitat and land cover mapping. Image segmentation plays a key role in GEOBIA workflows, allowing to partition images into homogenous and mutually exclusive regions. Nonetheless, segmentation techniques require a robust parameterization to achieve the best results. Frequently, inappropriate parameterization leads to sub-optimal results and difficulties in comparing distinct methods. Here, we present an approach based on Genetic Algorithms (GA) to optimize image segmentation parameters by using the performance scores from object-based classification, thus allowing to assess the adequacy of a segmented image in relation to the classification problem. This approach was implemented in a new R package called SegOptim, in which several segmentation algorithms are interfaced, mostly from open-source software (GRASS GIS, Orfeo Toolbox, RSGISLib, SAGA GIS, TerraLib), but also from proprietary software (ESRI ArcGIS). SegOptim also provides access to several machine-learning classification algorithms currently available in R, including Gradient Boosted Modelling, Support Vector Machines, and Random Forest. We tested our approach using very-high to high spatial resolution images collected from an Unmanned Aerial Vehicle (0.03 – 0.10 m), WorldView-2 (2 m), RapidEye (5 m) and Sentinel-2 (10 – 20 m) in six different test sites located in northern Portugal with varying environmental conditions and for different purposes, including invasive species detection and land cover mapping. The results highlight the added value of our novel comparison of image segmentation and classification algorithms. Overall classification performances (assessed through cross-validation with the Kappa index) ranged from 0.85 to 1.00. Pilot-tests show that our GA-based approach is capable of providing sound results for optimizing the parameters of different segmentation algorithms, with benefits for classification accuracy and for comparison across techniques. We also verified that no particular combination of an image segmentation and a classification algorithm is suited for all the tasks/objectives. Consequently, it is crucial to compare and optimize available methods to understand which one is more suited for a certain objective. Our approach allows a closer integration between the segmentation and classification stages, which is of high importance for GEOBIA workflows. The results from our tests confirm that this integration has benefits for comparing and optimizing both processes. We discuss some limitations of the SegOptim approach (and potential solutions) as well as a future roadmap to expand its current functionalities.

AB - Geographic Object-based Image Analysis (GEOBIA) is increasingly used to process high-spatial resolution imagery, with applications ranging from single species detection to habitat and land cover mapping. Image segmentation plays a key role in GEOBIA workflows, allowing to partition images into homogenous and mutually exclusive regions. Nonetheless, segmentation techniques require a robust parameterization to achieve the best results. Frequently, inappropriate parameterization leads to sub-optimal results and difficulties in comparing distinct methods. Here, we present an approach based on Genetic Algorithms (GA) to optimize image segmentation parameters by using the performance scores from object-based classification, thus allowing to assess the adequacy of a segmented image in relation to the classification problem. This approach was implemented in a new R package called SegOptim, in which several segmentation algorithms are interfaced, mostly from open-source software (GRASS GIS, Orfeo Toolbox, RSGISLib, SAGA GIS, TerraLib), but also from proprietary software (ESRI ArcGIS). SegOptim also provides access to several machine-learning classification algorithms currently available in R, including Gradient Boosted Modelling, Support Vector Machines, and Random Forest. We tested our approach using very-high to high spatial resolution images collected from an Unmanned Aerial Vehicle (0.03 – 0.10 m), WorldView-2 (2 m), RapidEye (5 m) and Sentinel-2 (10 – 20 m) in six different test sites located in northern Portugal with varying environmental conditions and for different purposes, including invasive species detection and land cover mapping. The results highlight the added value of our novel comparison of image segmentation and classification algorithms. Overall classification performances (assessed through cross-validation with the Kappa index) ranged from 0.85 to 1.00. Pilot-tests show that our GA-based approach is capable of providing sound results for optimizing the parameters of different segmentation algorithms, with benefits for classification accuracy and for comparison across techniques. We also verified that no particular combination of an image segmentation and a classification algorithm is suited for all the tasks/objectives. Consequently, it is crucial to compare and optimize available methods to understand which one is more suited for a certain objective. Our approach allows a closer integration between the segmentation and classification stages, which is of high importance for GEOBIA workflows. The results from our tests confirm that this integration has benefits for comparing and optimizing both processes. We discuss some limitations of the SegOptim approach (and potential solutions) as well as a future roadmap to expand its current functionalities.

KW - Genetic algorithms

KW - GEOBIA

KW - Geographic object-based image analysis

KW - High-spatial resolution

KW - Image segmentation

KW - Open-source software

KW - Optimization

KW - R package

KW - Supervised classification

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DO - 10.1016/j.jag.2018.11.011

M3 - Article

VL - 76

SP - 218

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JO - International Journal of applied Earth Observation and Geoinformation

JF - International Journal of applied Earth Observation and Geoinformation

SN - 0303-2434

ER -