scholarly journals GinJinn2: Object detection and segmentation for ecology and evolution

2021 ◽  
Author(s):  
Tankred Ott ◽  
Ulrich Lautenschlager
Keyword(s):  
Deep Learning ◽  
Object Detection ◽  
Image Data ◽  
Systematic Research ◽  
Herbarium Specimens ◽  
List Type ◽  
Learning Approaches ◽  
Advanced Analysis ◽  
User Friendly ◽  
Modern Machine

AbstractProper collection and preparation of empirical data still represent one of the most important, but also expensive steps in ecological and evolutionary/systematic research. Modern machine learning approaches, however, have the potential to automate a variety of tasks, which until recently could only be performed manually. Unfortunately, the application of such methods by researchers outside the field is hampered by technical difficulties, some of which, we believe, can be avoided.Here, we present GinJinn2, a user-friendly toolbox for deep learning-based object detection and instance segmentation on image data. Besides providing a convenient command-line interface to existing software libraries, it comprises several additional tools for data handling, pre- and postprocessing, and building advanced analysis pipelines.We demonstrate the application of GinJinn2 for biological purposes using four exemplary analyses, namely the evaluation of seed mixtures, detection of insects on glue traps, segmentation of stomata, and extraction of leaf silhouettes from herbarium specimens.GinJinn2 will enable users with a primary background in biology to apply deep learning-based methods for object detection and segmentation in order to automate feature extraction from image data.

scholarly journals U-Infuse: Democratization of Customizable AI for Object Detection

2020 ◽  
Author(s):  
Andrew Shepley ◽  
Greg Falzon ◽  
Christopher Lawson ◽  
Paul Meek ◽  
Paul Kwan
Keyword(s):  
Deep Learning ◽  
Object Detection ◽  
Image Data ◽  
Camera Trap ◽  
Learning Technologies ◽  
Training Data ◽  
List Type ◽  
Learning Models ◽  
Ecological Data ◽  
Large Numbers

SummaryImage data is one of the primary sources of ecological data used in biodiversity conservation and management worldwide. However, classifying and interpreting large numbers of images is time and resource expensive, particularly in the context of camera trapping. Deep learning models have been used to achieve this task but are often not suited to specific applications due to their inability to generalise to new environments and inconsistent performance. Models need to be developed for specific species cohorts and environments, but the technical skills required to achieve this are a key barrier to the accessibility of this technology to ecologists. There is a strong need to democratise access to deep learning technologies by providing an easy to use software application allowing non-technical users to custom train custom object detectors.U-Infuse addresses this issue by putting the power of AI into the hands of ecologists. U-Infuse provides ecologists with the ability to train customised models using publicly available images and/or their own camera trap images, without the constraints of annotating and pre-processing large numbers of images, or specific technical expertise. U-Infuse is a free and open-source software solution that supports both multiclass and single class training and inference, allowing ecologists to access state of the art AI on their own device, customised to their application without sharing IP or sensitive data.U-Infuse provides ecological practitioners with the ability to (i) easily achieve camera trap object detection within a user-friendly GUI, generating a species distribution report, and other useful statistics, (ii) custom train deep learning models using publicly available and custom training data, (iii) achieve supervised auto-annotation of images for further training, with the benefit of editing annotations to ensure quality datasets.Broad adoption of U-Infuse by ecological practitioners will improve camera trap image analysis and processing by allowing significantly more image data to be processed with minimal expenditure of time and resources. Ease of training and reliance on transfer learning means domain-specific models can be trained rapidly, and frequently updated without the need for computer science expertise, or data sharing, protecting intellectual property and privacy.

Deep Learning Approaches for Whiteboard Image Quality Enhancement

2019 ◽  
Vol 2019 (1) ◽  
pp. 360-368
Author(s):  
Mekides Assefa Abebe ◽  
Jon Yngve Hardeberg
Keyword(s):  
Deep Learning ◽  
Image Quality ◽  
Image Data ◽  
Quality Enhancement ◽  
Network Architectures ◽  
Learning Approaches ◽  
Data Set ◽  
Image Quality Enhancement ◽  
Processing Techniques ◽  
White Balancing

Different whiteboard image degradations highly reduce the legibility of pen-stroke content as well as the overall quality of the images. Consequently, different researchers addressed the problem through different image enhancement techniques. Most of the state-of-the-art approaches applied common image processing techniques such as background foreground segmentation, text extraction, contrast and color enhancements and white balancing. However, such types of conventional enhancement methods are incapable of recovering severely degraded pen-stroke contents and produce artifacts in the presence of complex pen-stroke illustrations. In order to surmount such problems, the authors have proposed a deep learning based solution. They have contributed a new whiteboard image data set and adopted two deep convolutional neural network architectures for whiteboard image quality enhancement applications. Their different evaluations of the trained models demonstrated their superior performances over the conventional methods.

scholarly journals U-Infuse: Democratization of Customizable Deep Learning for Object Detection

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2611
Author(s):  
Andrew Shepley ◽  
Greg Falzon ◽  
Christopher Lawson ◽  
Paul Meek ◽  
Paul Kwan
Keyword(s):  
Deep Learning ◽  
Intellectual Property ◽  
Object Detection ◽  
Image Data ◽  
Learning Technologies ◽  
Training Data ◽  
Learning Models ◽  
Ecological Data ◽  
Single Class ◽  
Large Numbers

Image data is one of the primary sources of ecological data used in biodiversity conservation and management worldwide. However, classifying and interpreting large numbers of images is time and resource expensive, particularly in the context of camera trapping. Deep learning models have been used to achieve this task but are often not suited to specific applications due to their inability to generalise to new environments and inconsistent performance. Models need to be developed for specific species cohorts and environments, but the technical skills required to achieve this are a key barrier to the accessibility of this technology to ecologists. Thus, there is a strong need to democratize access to deep learning technologies by providing an easy-to-use software application allowing non-technical users to train custom object detectors. U-Infuse addresses this issue by providing ecologists with the ability to train customised models using publicly available images and/or their own images without specific technical expertise. Auto-annotation and annotation editing functionalities minimize the constraints of manually annotating and pre-processing large numbers of images. U-Infuse is a free and open-source software solution that supports both multiclass and single class training and object detection, allowing ecologists to access deep learning technologies usually only available to computer scientists, on their own device, customised for their application, without sharing intellectual property or sensitive data. It provides ecological practitioners with the ability to (i) easily achieve object detection within a user-friendly GUI, generating a species distribution report, and other useful statistics, (ii) custom train deep learning models using publicly available and custom training data, (iii) achieve supervised auto-annotation of images for further training, with the benefit of editing annotations to ensure quality datasets. Broad adoption of U-Infuse by ecological practitioners will improve ecological image analysis and processing by allowing significantly more image data to be processed with minimal expenditure of time and resources, particularly for camera trap images. Ease of training and use of transfer learning means domain-specific models can be trained rapidly, and frequently updated without the need for computer science expertise, or data sharing, protecting intellectual property and privacy.

scholarly journals A Survey of Graphical Page Object Detection with Deep Neural Networks

2021 ◽  
Author(s):  
Jwalin Bhatt ◽  
Khurram Azeem Hashmi ◽  
Muhammad Zeshan Afzal ◽  
Didier Stricker
Keyword(s):  
Deep Learning ◽  
Object Detection ◽  
Conceptual Understanding ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Learning Approaches ◽  
Document Images ◽  
Essential Information ◽  
Current State ◽  
High Level

In any document, graphical elements like tables, figures, and formulas contain essential information. The processing and interpretation of such information require specialized algorithms. Off-the-shelf OCR components cannot process this information reliably. Therefore, an essential step in document analysis pipelines is to detect these graphical components. It leads to a high-level conceptual understanding of the documents that makes digitization of documents viable. Since the advent of deep learning, the performance of deep learning-based object detection has improved many folds. In this work, we outline and summarize the deep learning approaches for detecting graphical page objects in the document images. Therefore, we discuss the most relevant deep learning-based approaches and state-of-the-art graphical page object detection in document images. This work provides a comprehensive understanding of the current state-of-the-art and related challenges. Furthermore, we discuss leading datasets along with the quantitative evaluation. Moreover, it discusses briefly the promising directions that can be utilized for further improvements.

Comparison of Object Detection Methods for Corn Damage Assessment Using Deep Learning

2020 ◽  
Vol 63 (6) ◽  
pp. 1969-1980
Author(s):  
Ali Hamidisepehr ◽  
Seyed V. Mirnezami ◽  
Jason K. Ward
Keyword(s):  
Computer Vision ◽  
Deep Learning ◽  
Object Detection ◽  
Damage Detection ◽  
Damage Identification ◽  
Severe Weather ◽  
Crop Damage ◽  
Growth Stages ◽  
List Type ◽  
Data Set

HighlightsCorn damage detection was possible using advanced deep learning and computer vision techniques trained with images of simulated corn lodging.RetinaNet and YOLOv2 both worked well at identifying regions of lodged corn.Automating crop damage identification could provide useful information to producers and other stakeholders from visual-band UAS imagery.Abstract. Severe weather events can cause large financial losses to farmers. Detailed information on the location and severity of damage will assist farmers, insurance companies, and disaster response agencies in making wise post-damage decisions. The goal of this study was a proof-of-concept to detect areas of damaged corn from aerial imagery using computer vision and deep learning techniques. A specific objective was to compare existing object detection algorithms to determine which is best suited for corn damage detection. Simulated corn lodging was used to create a training and analysis data set. An unmanned aerial system equipped with an RGB camera was used for image acquisition. Three popular object detectors (Faster R-CNN, YOLOv2, and RetinaNet) were assessed for their ability to detect damaged areas. Average precision (AP) was used to compare object detectors. RetinaNet and YOLOv2 demonstrated robust capability for corn damage identification, with AP ranging from 98.43% to 73.24% and from 97.0% to 55.99%, respectively, across all conditions. Faster R-CNN did not perform as well as the other two models, with AP between 77.29% and 14.47% for all conditions. Detecting corn damage at later growth stages was more difficult for all three object detectors. Keywords: Computer vision, Faster R-CNN, RetinaNet, Severe weather, Smart farming, YOLO.

scholarly journals MethylNet: An Automated and Modular Deep Learning Approach for DNA Methylation Analysis

2019 ◽  
Author(s):  
Joshua J. Levy ◽  
Alexander J. Titus ◽  
Curtis L. Petersen ◽  
Youdinghuan Chen ◽  
Lucas A. Salas ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Deep Learning ◽  
Multiple Hypothesis Testing ◽  
Cellular Heterogeneity ◽  
Learning Approaches ◽  
Disease Heterogeneity ◽  
Epigenetic Regulator ◽  
User Friendly ◽  
Dna Methylation Analysis ◽  
Linear Nature

AbstractBackgroundDNA methylation (DNAm) is an epigenetic regulator of gene expression programs that can be altered by environmental exposures, aging, and in pathogenesis. Traditional analyses that associate DNAm alterations with phenotypes suffer from multiple hypothesis testing and multi-collinearity due to the high-dimensional, continuous, interacting and non-linear nature of the data. Deep learning analyses have shown much promise to study disease heterogeneity. DNAm deep learning approaches have not yet been formalized into user-friendly frameworks for execution, training, and interpreting models. Here, we describe MethylNet, a DNAm deep learning method that can construct embeddings, make predictions, generate new data, and uncover unknown heterogeneity with minimal user supervision.ResultsThe results of our experiments indicate that MethylNet can study cellular differences, grasp higher order information of cancer sub-types, estimate age and capture factors associated with smoking in concordance with known differences.ConclusionThe ability of MethylNet to capture nonlinear interactions presents an opportunity for further study of unknown disease, cellular heterogeneity and aging processes.

scholarly journals Deep Learning Approaches for Object Detection

2020 ◽  
pp. 123-145
Author(s):  
Sushma Jaiswal ◽  
Tarun Jaiswal
Keyword(s):  
Deep Learning ◽  
Object Detection ◽  
Autonomous Driving ◽  
General Idea ◽  
Detection Methods ◽  
Learning Approaches ◽  
Detection Techniques ◽  
Second Stage ◽  
Fast Pace ◽  
Benchmark Datasets

In computer vision, object detection is a very important, exciting and mind-blowing study. Object detection work in numerous fields such as observing security, independently/autonomous driving and etc. Deep-learning based object detection techniques have developed at a very fast pace and have attracted the attention of many researchers. The main focus of the 21st century is the development of the object-detection framework, comprehensively and genuinely. In this investigation, we initially investigate and evaluate the various object detection approaches and designate the benchmark datasets. We also delivered the wide-ranging general idea of object detection approaches in an organized way. We covered the first and second stage detectors of object detection methods. And lastly, we consider the construction of these object detection approaches to give dimensions for further research.

scholarly journals Improved Method to Detect the Tailings Ponds from Multispectral Remote Sensing Images Based on Faster R-CNN and Transfer Learning

2021 ◽  
Vol 14 (1) ◽  
pp. 103
Author(s):  
Dongchuan Yan ◽  
Hao Zhang ◽  
Guoqing Li ◽  
Xiangqiang Li ◽  
Hua Lei ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Deep Learning ◽  
Object Detection ◽  
Transfer Learning ◽  
Near Infrared ◽  
Image Data ◽  
Remote Sensing Images ◽  
Tailings Pond ◽  
True Color ◽  
Tailings Ponds

The breaching of tailings pond dams may lead to casualties and environmental pollution; therefore, timely and accurate monitoring is an essential aspect of managing such structures and preventing accidents. Remote sensing technology is suitable for the regular extraction and monitoring of tailings pond information. However, traditional remote sensing is inefficient and unsuitable for the frequent extraction of large volumes of highly precise information. Object detection, based on deep learning, provides a solution to this problem. Most remote sensing imagery applications for tailings pond object detection using deep learning are based on computer vision, utilizing the true-color triple-band data of high spatial resolution imagery for information extraction. The advantage of remote sensing image data is their greater number of spectral bands (more than three), providing more abundant spectral information. There is a lack of research on fully harnessing multispectral band information to improve the detection precision of tailings ponds. Accordingly, using a sample dataset of tailings pond satellite images from the Gaofen-1 high-resolution Earth observation satellite, we improved the Faster R-CNN deep learning object detection model by increasing the inputs from three true-color bands to four multispectral bands. Moreover, we used the attention mechanism to recalibrate the input contributions. Subsequently, we used a step-by-step transfer learning method to improve and gradually train our model. The improved model could fully utilize the near-infrared (NIR) band information of the images to improve the precision of tailings pond detection. Compared with that of the three true-color band input models, the tailings pond detection average precision (AP) and recall notably improved in our model, with the AP increasing from 82.3% to 85.9% and recall increasing from 65.4% to 71.9%. This research could serve as a reference for using multispectral band information from remote sensing images in the construction and application of deep learning models.

scholarly journals Nuances of Interpreting X-ray Analysis by Deep Learning and Lessons for Reporting Experimental Findings

Sci ◽  
2022 ◽  
Vol 4 (1) ◽  
pp. 3
Author(s):  
Steinar Valsson ◽  
Ognjen Arandjelović
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Spatial Information ◽  
Characteristic Curve ◽  
Image Data ◽  
Qualitative Assessment ◽  
Learning Approaches ◽  
Clinical Value ◽  
Diagnostic Significance ◽  
X Ray

With the increase in the availability of annotated X-ray image data, there has been an accompanying and consequent increase in research on machine-learning-based, and ion particular deep-learning-based, X-ray image analysis. A major problem with this body of work lies in how newly proposed algorithms are evaluated. Usually, comparative analysis is reduced to the presentation of a single metric, often the area under the receiver operating characteristic curve (AUROC), which does not provide much clinical value or insight and thus fails to communicate the applicability of proposed models. In the present paper, we address this limitation of previous work by presenting a thorough analysis of a state-of-the-art learning approach and hence illuminate various weaknesses of similar algorithms in the literature, which have not yet been fully acknowledged and appreciated. Our analysis was performed on the ChestX-ray14 dataset, which has 14 lung disease labels and metainfo such as patient age, gender, and the relative X-ray direction. We examined the diagnostic significance of different metrics used in the literature including those proposed by the International Medical Device Regulators Forum, and present the qualitative assessment of the spatial information learned by the model. We show that models that have very similar AUROCs can exhibit widely differing clinical applicability. As a result, our work demonstrates the importance of detailed reporting and analysis of the performance of machine-learning approaches in this field, which is crucial both for progress in the field and the adoption of such models in practice.

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