scholarly journals A Generalised Approach for High-throughput Instance Segmentation of Stomata in Microscope Images

2020 ◽  
Author(s):  
Hiranya Samanga Jayakody ◽  
Paul Petrie ◽  
Hugo de Boer ◽  
Mark Whitty
Keyword(s):  
High Throughput ◽  
Imaging Techniques ◽  
Detection Algorithm ◽  
Input Image ◽  
Detection Methods ◽  
Sample Collection ◽  
High Throughput Analysis ◽  
General Applicability ◽  
Additional Image ◽  
Bounding Boxes

Abstract Background: Stomata analysis using microscope imagery provides important insight into plant physiology, health and the surrounding environmental conditions. Plant scientists are now able to conduct automated high-throughput analysis of stomata in microscope data, however, existing detection methods are sensitive to the appearance of stomata in the training images, thereby limiting general applicability. In addition, existing methods only generate bounding-boxes around detected stomata, which require users to implement additional image processing steps to study stomata morphology. In this paper, we develop a fully automated, robust stomata detection algorithm which can also identify individual stomata boundaries regardless of the plant species, sample collection method, imaging technique and magnification level. Results: The proposed solution consists of three stages. First, the input image is pre-processed to remove any colour space biases occurring from different sample collection and imaging techniques. Then, a Mask R-CNN is applied to estimate individual stomata boundaries. The feature pyramid network embedded in the Mask R-CNN is utilised to identify stomata at different scales. Finally, a statistical filter is implemented at the Mask R-CNN output to reduce the number of false positive generated by the network. The algorithm was tested using 16 datasets from 12 sources, containing over 60,000 stomata. For the first time in this domain, the proposed solution was tested against 7 microscope datasets never seen by the algorithm to show the generalisability of the solution. Results indicated that the proposed approach can detect stomata with a precision, recall, and F-score of 95.10\%, 83.34\%, and 88.61\%, respectively. A separate test conducted by comparing estimated stomata boundary values with manually measured data showed that the proposed method has an IoU score of 0.70; a 7\% improvement over the bounding-box approach. Conclusions: The proposed method shows robust performance across multiple microscope image datasets of different quality and scale. This generalised stomata detection algorithm allows plant scientists to conduct stomata analysis whilst eliminating the need to re-label and re-train for each new dataset. The open-source code shared with this project can be directly deployed in Google Colab or any other Tensorflow environment.

scholarly journals A generalised approach for high-throughput instance segmentation of stomata in microscope images

Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Hiranya Jayakody ◽  
Paul Petrie ◽  
Hugo Jan de Boer ◽  
Mark Whitty
Keyword(s):  
High Throughput ◽  
Imaging Techniques ◽  
Detection Algorithm ◽  
Input Image ◽  
Detection Methods ◽  
Sample Collection ◽  
High Throughput Analysis ◽  
General Applicability ◽  
Additional Image ◽  
Bounding Boxes

Abstract Background Stomata analysis using microscope imagery provides important insight into plant physiology, health and the surrounding environmental conditions. Plant scientists are now able to conduct automated high-throughput analysis of stomata in microscope data, however, existing detection methods are sensitive to the appearance of stomata in the training images, thereby limiting general applicability. In addition, existing methods only generate bounding-boxes around detected stomata, which require users to implement additional image processing steps to study stomata morphology. In this paper, we develop a fully automated, robust stomata detection algorithm which can also identify individual stomata boundaries regardless of the plant species, sample collection method, imaging technique and magnification level. Results The proposed solution consists of three stages. First, the input image is pre-processed to remove any colour space biases occurring from different sample collection and imaging techniques. Then, a Mask R-CNN is applied to estimate individual stomata boundaries. The feature pyramid network embedded in the Mask R-CNN is utilised to identify stomata at different scales. Finally, a statistical filter is implemented at the Mask R-CNN output to reduce the number of false positive generated by the network. The algorithm was tested using 16 datasets from 12 sources, containing over 60,000 stomata. For the first time in this domain, the proposed solution was tested against 7 microscope datasets never seen by the algorithm to show the generalisability of the solution. Results indicated that the proposed approach can detect stomata with a precision, recall, and F-score of 95.10%, 83.34%, and 88.61%, respectively. A separate test conducted by comparing estimated stomata boundary values with manually measured data showed that the proposed method has an IoU score of 0.70; a 7% improvement over the bounding-box approach. Conclusions The proposed method shows robust performance across multiple microscope image datasets of different quality and scale. This generalised stomata detection algorithm allows plant scientists to conduct stomata analysis whilst eliminating the need to re-label and re-train for each new dataset. The open-source code shared with this project can be directly deployed in Google Colab or any other Tensorflow environment.

scholarly journals A Generalised Approach for High-throughput Instance Segmentation of Stomata in Microscope Images

2020 ◽  
Author(s):  
Hiranya Samanga Jayakody ◽  
Paul Petrie ◽  
Hugo de Boer ◽  
Mark Whitty
Keyword(s):  
High Throughput ◽  
Imaging Techniques ◽  
Detection Algorithm ◽  
Input Image ◽  
Detection Methods ◽  
Sample Collection ◽  
High Throughput Analysis ◽  
General Applicability ◽  
Additional Image ◽  
Bounding Boxes

Abstract Background: Stomata analysis using microscope imagery provides important insight into plant physiology, health and the surrounding environmental conditions. Plant scientists are now able to conduct automated high-throughput analysis of stomata in microscope data, however, existing detection methods are sensitive to the appearance of stomata in the training images, thereby limiting general applicability. In addition, existing methods only generate bounding-boxes around detected stomata, which require users to implement additional image processing steps to study stomata morphology. In this paper, we develop a fully automated, robust stomata detection algorithm which can also identify individual stomata boundaries regardless of the plant species, sample collection method, imaging technique and magnification level. Results: The proposed solution consists of three stages. Firstly, the input image is pre-processed to remove any colour-space biases occurring from different sample collection and imaging techniques. Secondly, a Mask R-CNN is applied to estimate individual stomata boundaries and the feature pyramid network embedded in the Mask R-CNN allows the network to identify stomata at different scales. Finally, a statistical filter is implemented at the Mask R-CNN output to reduce the number of false positive generated by the network. The algorithm was tested using 16 datasets from 12 sources, containing over 60,000 stomata. For the first time in this domain, the proposed solution was tested against 7 microscope datasets never seen by the algorithm to show the generalisability of the solution. Results indicated that the proposed approach can detect stomata with a precision, recall, and F-score of 95.10%, 83.34%, and 88.61%, respectively. A separate test conducted by comparing estimated stomata boundary values with manually measured data showed that the proposed method has an IoU score of 0.70; a 7% improvement over the bounding-box approach. Conclusion: The proposed method shows robust performance across multiple microscope image datasets of different quality and scale. This generalised stomata detection algorithm allows plant scientists to conduct stomata analysis whilst eliminating the need to re-label and re-train for each new dataset. The open-source code for the project can be directly deployed in Google Colab or any other Tensorflow environment.

scholarly journals A Generalised Approach for High-throughput Instance Segmentation of Stomata in Microscope Images

2020 ◽  
Author(s):  
Hiranya Samanga Jayakody ◽  
Paul Petrie ◽  
Hugo de Boer ◽  
Mark Whitty
Keyword(s):  
High Throughput ◽  
Imaging Techniques ◽  
Detection Algorithm ◽  
Input Image ◽  
Detection Methods ◽  
Sample Collection ◽  
High Throughput Analysis ◽  
General Applicability ◽  
Additional Image ◽  
Bounding Boxes

Abstract Background: Stomata analysis using microscope imagery provides important insight into plant physiology, health and the surrounding environmental conditions. Plant scientists are now able to conduct automated high-throughput analysis of stomata in microscope data, however, existing detection methods are sensitive to the appearance of stomata in the training images, thereby limiting general applicability. In addition, existing methods only generate bounding-boxes around detected stomata, which require users to implement additional image processing steps to study stomata morphology. In this paper, we develop a fully automated, robust stomata detection algorithm which can also identify individualstomata boundaries regardless of the plant species, sample collection method, imaging technique and magnfication level.Results: The proposed solution consists of three stages. First, the input image is pre-processed to remove any colour space biases occurring from different sample collection and imaging techniques. Then, a Mask R-CNN is applied to estimate individual stomata boundaries. The feature pyramid network embedded in the Mask R-CNN is utilised to identify stomata at different scales. Finally, a statistical lter is implemented at the Mask R-CNN output to reduce the number of false positive generated by the network.The algorithm was tested using 16 datasets from 12 sources, containing over 60,000 stomata. For the rst time in this domain, the proposed solution was tested against 7 microscope datasets never seen by the algorithm to show the generalisability of the solution. Results indicated that the proposed approach can detect stomata with a precision, recall, and F-score of 95.10%, 83.34%, and 88.61%, respectively. A separate test conducted by comparing estimated stomata boundary values with manually measured data showed that the proposed method has an IoU score of 0.70; a 7% improvement over the bounding-box approach.Conclusions: The proposed method shows robust performance across multiple microscope image datasets of different quality and scale. This generalised stomata detection algorithm allows plant scientists to conduct stomata analysis whilst eliminating the need to re-label and re-train for each new dataset. The open-source code shared with this project can be directly deployed in Google Colab or any other Tensorflow environment.

scholarly journals Robust Cherry Tomatoes Detection Algorithm in Greenhouse Scene Based on SSD

Agriculture ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 160
Author(s):  
Ting Yuan ◽  
Lin Lv ◽  
Fan Zhang ◽  
Jun Fu ◽  
Jin Gao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Detection Algorithm ◽  
Input Image ◽  
Detection Methods ◽  
Single Shot ◽  
Image Size ◽  
Growth Difference ◽  
Input Size ◽  
Base Network ◽  
Cherry Tomatoes

The detection of cherry tomatoes in greenhouse scene is of great significance for robotic harvesting. This paper states a method based on deep learning for cherry tomatoes detection to reduce the influence of illumination, growth difference, and occlusion. In view of such greenhouse operating environment and accuracy of deep learning, Single Shot multi-box Detector (SSD) was selected because of its excellent anti-interference ability and self-taught from datasets. The first step is to build datasets containing various conditions in greenhouse. According to the characteristics of cherry tomatoes, the image samples with illumination change, images rotation and noise enhancement were used to expand the datasets. Then training datasets were used to train and construct network model. To study the effect of base network and the input size of networks, one contrast experiment was designed on different base networks of VGG16, MobileNet, Inception V2 networks, and the other contrast experiment was conducted on changing the network input image size of 300 pixels by 300 pixels, 512 pixels by 512 pixels. Through the analysis of the experimental results, it is found that the Inception V2 network is the best base network with the average precision of 98.85% in greenhouse environment. Compared with other detection methods, this method shows substantial improvement in cherry tomatoes detection.

scholarly journals An Efficient Document Skew Detection Method Using Probability Model and Q Test

Electronics ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 55
Author(s):  
Kai Huang ◽  
Zixuan Chen ◽  
Min Yu ◽  
Xiaolang Yan ◽  
Aiguo Yin
Keyword(s):  
High Speed ◽  
Probability Model ◽  
Detection Algorithm ◽  
Detection Methods ◽  
Connected Components ◽  
Skew Angle ◽  
Skew Detection ◽  
Detection Approach ◽  
And Performance ◽  
Bounding Boxes

Document skew detection is one of the key technologies in most of the document analysis systems. However, existing skew detection methods either have low accuracy or require a large amount of computation. To achieve a good tradeoff between efficiency and performance, we propose a novel skew detection approach based on bounding boxes, probability model, and Dixon’s Q test. Firstly, bounding boxes are used to pick out the eligible connected components (ECC). Then, we calculate the slopes of the skew document with the probability model. Finally, we find the optimal result with Dixon’s Q test and projection profile method. Moreover, the proposed method can detect the skew angle in a wider range. The experimental results show that our skew detection algorithm can achieve high speed and accuracy simultaneously compared with existing algorithms.

scholarly journals R-YOLO: A Real-Time Text Detector for Natural Scenes with Arbitrary Rotation

Sensors ◽  
2021 ◽  
Vol 21 (3) ◽  
pp. 888
Author(s):  
Xiqi Wang ◽  
Shunyi Zheng ◽  
Ce Zhang ◽  
Rui Li ◽  
Li Gui
Keyword(s):  
Real Time ◽  
Detection Efficiency ◽  
Input Image ◽  
Text Detection ◽  
Detection Methods ◽  
Natural Image ◽  
Natural Scenes ◽  
Novel Method ◽  
Bounding Boxes ◽  
Image Streams

Accurate and efficient text detection in natural scenes is a fundamental yet challenging task in computer vision, especially when dealing with arbitrarily-oriented texts. Most contemporary text detection methods are designed to identify horizontal or approximately horizontal text, which cannot satisfy practical detection requirements for various real-world images such as image streams or videos. To address this lacuna, we propose a novel method called Rotational You Only Look Once (R-YOLO), a robust real-time convolutional neural network (CNN) model to detect arbitrarily-oriented texts in natural image scenes. First, a rotated anchor box with angle information is used as the text bounding box over various orientations. Second, features of various scales are extracted from the input image to determine the probability, confidence, and inclined bounding boxes of the text. Finally, Rotational Distance Intersection over Union Non-Maximum Suppression is used to eliminate redundancy and acquire detection results with the highest accuracy. Experiments on benchmark comparison are conducted upon four popular datasets, i.e., ICDAR2015, ICDAR2013, MSRA-TD500, and ICDAR2017-MLT. The results indicate that the proposed R-YOLO method significantly outperforms state-of-the-art methods in terms of detection efficiency while maintaining high accuracy; for example, the proposed R-YOLO method achieves an F-measure of 82.3% at 62.5 fps with 720 p resolution on the ICDAR2015 dataset.

scholarly journals Object Detection Algorithm Based on Improved YOLOv3

Electronics ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 537 ◽  
Author(s):  
Liquan Zhao ◽  
Shuaiyang Li
Keyword(s):  
Markov Chains ◽  
Object Detection ◽  
Large Scale ◽  
Ground Truth ◽  
Detection Algorithm ◽  
Detection Methods ◽  
Cluster Method ◽  
Cluster Center ◽  
Initial Cluster ◽  
Bounding Boxes

The ‘You Only Look Once’ v3 (YOLOv3) method is among the most widely used deep learning-based object detection methods. It uses the k-means cluster method to estimate the initial width and height of the predicted bounding boxes. With this method, the estimated width and height are sensitive to the initial cluster centers, and the processing of large-scale datasets is time-consuming. In order to address these problems, a new cluster method for estimating the initial width and height of the predicted bounding boxes has been developed. Firstly, it randomly selects a couple of width and height values as one initial cluster center separate from the width and height of the ground truth boxes. Secondly, it constructs Markov chains based on the selected initial cluster and uses the final points of every Markov chain as the other initial centers. In the construction of Markov chains, the intersection-over-union method is used to compute the distance between the selected initial clusters and each candidate point, instead of the square root method. Finally, this method can be used to continually update the cluster center with each new set of width and height values, which are only a part of the data selected from the datasets. Our simulation results show that the new method has faster convergence speed for initializing the width and height of the predicted bounding boxes and that it can select more representative initial widths and heights of the predicted bounding boxes. Our proposed method achieves better performance than the YOLOv3 method in terms of recall, mean average precision, and F1-score.

scholarly journals One-Stage Anchor-Free 3D Vehicle Detection from LiDAR Sensors

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2651
Author(s):  
Hao Li ◽  
Sanyuan Zhao ◽  
Wenjun Zhao ◽  
Libin Zhang ◽  
Jianbing Shen
Keyword(s):  
Single Channel ◽  
Ground Plane ◽  
Orientation Angle ◽  
Region Of Interest ◽  
Vehicle Detection ◽  
Point Clouds ◽  
Detection Algorithm ◽  
Detection Methods ◽  
One Stage ◽  
Bounding Boxes

Recent one-stage 3D detection methods generate anchor boxes with various sizes and orientations in the ground plane, then determine whether these anchor boxes contain any region of interest and adjust the edges of them for accurate object bounding boxes. The anchor-based algorithm calculates the classification and regression label for each anchor box during the training process, which is inefficient and complicated. We propose a one-stage, anchor-free 3D vehicle detection algorithm based on LiDAR point clouds. The object position is encoded as a set of keypoints in the bird’s-eye view (BEV) of point clouds. We apply the voxel/pillar feature extractor and convolutional blocks to map an unstructured point cloud to a single-channel 2D heatmap. The vehicle’s Z-axis position, dimension, and orientation angle are regressed as additional attributes of the keypoints. Our method combines SmoothL1 loss and IoU (Intersection over Union) loss, and we apply (cosθ,sinθ) as angle regression labels, which achieve high average orientation similarity (AOS) without any direction classification tricks. During the target assignment and bounding box decoding process, our framework completely avoids any calculations related to anchor boxes. Our framework is end-to-end training and stands at the same performance level as the other one-stage anchor-based detectors.

scholarly journals LRP-DS: Lightweight RepPoints with Decoupled Sampling Point Set

2021 ◽  
Vol 11 (13) ◽  
pp. 5876
Author(s):  
Jinchao Wang ◽  
Libo Weng ◽  
Fei Gao
Keyword(s):  
Sampling Method ◽  
Input Image ◽  
Detection Methods ◽  
Sampling Point ◽  
Localization Accuracy ◽  
Backbone Network ◽  
Point Set ◽  
The Difference ◽  
Bounding Boxes ◽  
Representative Points

Most object detection methods use rectangular bounding boxes to represent the object, while the representative points network (RepPoints) employs a point set to describe the object. The RepPoints can provide more fine-grained localization and facilitates classification. However, it ignores the difference between localization and classification tasks. Therefore, a lightweight RepPoints with decoupling of the sampling point set (LRP-DS) is proposed in this paper. Firstly, the lightweight MobileNet-V2 and Feature Pyramid Networks (FPN) is employed as the backbone network to realize the lightweight network, rather than the Resnet. Secondly, considering the difference between classification and localization tasks, the sampling points of classification and localization are decoupled, by introducing classification free sampling method. Finally, due to the introduction of the classification free sampling method, the problem of the mismatch between the localization accuracy and the classification confidence is highlighted, so the localization score is employed to describe the localization accuracy independently. The final network structure of this paper achieves 73.3% mean average precision (mAP) on the VOC07 test dataset, which is 1.9% higher than original RepPoints with the same backbone network MobileNetV2 and FPN. Our LRP-DS has a detection speed of 20FPS for the input image of (1000, 600), on RTX2060 GPU, which is nearly twice as fast as the backbone network of ResNet50 and FPN. Experimental results show the effectiveness of our method.

Sign in / Sign up

Export Citation Format

Share Document