scholarly journals Digitally deconstructing leaves in 3D using X‐ray microcomputed tomography and machine learning

2020 ◽  
Vol 8 (7) ◽  
Author(s):  
Guillaume Théroux‐Rancourt ◽  
Matthew R. Jenkins ◽  
Craig R. Brodersen ◽  
Andrew McElrone ◽  
Elisabeth J. Forrestel ◽  
...  
2019 ◽  
Vol 142 ◽  
pp. 105882 ◽  
Author(s):  
Pratama Istiadi Guntoro ◽  
Glacialle Tiu ◽  
Yousef Ghorbani ◽  
Cecilia Lund ◽  
Jan Rosenkranz

2019 ◽  
Author(s):  
Guillaume Théroux-Rancourt ◽  
Matthew R. Jenkins ◽  
Craig R. Brodersen ◽  
Andrew McElrone ◽  
Elisabeth J. Forrestel ◽  
...  

ABSTRACTPremise of the studyX-ray microcomputed tomography (microCT) can be used to measure 3D leaf internal anatomy, providing a holistic view of tissue organisation. Previously, the substantial time needed for segmenting multiple tissues limited this technique to small datasets, restricting its utility for phenotyping experiments and limiting our confidence in the conclusion of these studies due to low replication numbers.Methods and ResultsWe present a Python codebase for random-forest machine learning segmentation and 3D leaf anatomical trait quantification which dramatically reduces the time required to process single leaf microCT scans into detailed segmentations. By training the model on each scan using 6 hand segmented image slices out of >1500 in the full leaf scan, it achieves >90% accuracy in background and tissue segmentation.ConclusionOverall, this 3D segmentation and quantification pipeline can reduce one of the major barriers to using microCT imaging in high-throughput plant phenotyping.


2021 ◽  
Author(s):  
Sascha Senck ◽  
Michael Happl ◽  
Michael Scheerer ◽  
Jonathan Glinz ◽  
Thomas Reiter ◽  
...  

Energies ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4595
Author(s):  
Parisa Asadi ◽  
Lauren E. Beckingham

X-ray CT imaging provides a 3D view of a sample and is a powerful tool for investigating the internal features of porous rock. Reliable phase segmentation in these images is highly necessary but, like any other digital rock imaging technique, is time-consuming, labor-intensive, and subjective. Combining 3D X-ray CT imaging with machine learning methods that can simultaneously consider several extracted features in addition to color attenuation, is a promising and powerful method for reliable phase segmentation. Machine learning-based phase segmentation of X-ray CT images enables faster data collection and interpretation than traditional methods. This study investigates the performance of several filtering techniques with three machine learning methods and a deep learning method to assess the potential for reliable feature extraction and pixel-level phase segmentation of X-ray CT images. Features were first extracted from images using well-known filters and from the second convolutional layer of the pre-trained VGG16 architecture. Then, K-means clustering, Random Forest, and Feed Forward Artificial Neural Network methods, as well as the modified U-Net model, were applied to the extracted input features. The models’ performances were then compared and contrasted to determine the influence of the machine learning method and input features on reliable phase segmentation. The results showed considering more dimensionality has promising results and all classification algorithms result in high accuracy ranging from 0.87 to 0.94. Feature-based Random Forest demonstrated the best performance among the machine learning models, with an accuracy of 0.88 for Mancos and 0.94 for Marcellus. The U-Net model with the linear combination of focal and dice loss also performed well with an accuracy of 0.91 and 0.93 for Mancos and Marcellus, respectively. In general, considering more features provided promising and reliable segmentation results that are valuable for analyzing the composition of dense samples, such as shales, which are significant unconventional reservoirs in oil recovery.


2021 ◽  
Vol 143 (10) ◽  
pp. 3779-3793
Author(s):  
Paula C. Ortet ◽  
Samantha N. Muellers ◽  
Lauren A. Viarengo-Baker ◽  
Kristina Streu ◽  
Blair R. Szymczyna ◽  
...  

2021 ◽  
pp. 115152
Author(s):  
Mahbubunnabi Tamal ◽  
Maha Alshammari ◽  
Meernah Alabdullah ◽  
Rana Hourani ◽  
Hossain Abu Alola ◽  
...  

Author(s):  
Ali Guven ◽  
Imam Samil Yetik ◽  
Ahmet Culhaoglu ◽  
Kaan Orhan ◽  
Mehmet Kilicarslan Kilicarslan
Keyword(s):  

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