scholarly journals A Deep Learning Instance Segmentation Approach for Global Glomerulosclerosis Assessment in Donor Kidney Biopsies

Electronics ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1768
Author(s):  
Nicola Altini ◽  
Giacomo Donato Cascarano ◽  
Antonio Brunetti ◽  
Irio De Feudis ◽  
Domenico Buongiorno ◽  
...  
Keyword(s):  
Deep Learning ◽  
Semantic Segmentation ◽  
Point Of View ◽  
University Hospital ◽  
Kidney Section ◽  
Global Glomerulosclerosis ◽  
Bounding Boxes ◽  
F Measure ◽  
Instance Segmentation

The histological assessment of glomeruli is fundamental for determining if a kidney is suitable for transplantation. The Karpinski score is essential to evaluate the need for a single or dual kidney transplant and includes the ratio between the number of sclerotic glomeruli and the overall number of glomeruli in a kidney section. The manual evaluation of kidney biopsies performed by pathologists is time-consuming and error-prone, so an automatic framework to delineate all the glomeruli present in a kidney section can be very useful. Our experiments have been conducted on a dataset provided by the Department of Emergency and Organ Transplantations (DETO) of Bari University Hospital. This dataset is composed of 26 kidney biopsies coming from 19 donors. The rise of Convolutional Neural Networks (CNNs) has led to a realm of methods which are widely applied in Medical Imaging. Deep learning techniques are also very promising for the segmentation of glomeruli, with a variety of existing approaches. Many methods only focus on semantic segmentation—which consists in segmentation of individual pixels—or ignore the problem of discriminating between non-sclerotic and sclerotic glomeruli, so these approaches are not optimal or inadequate for transplantation assessment. In this work, we employed an end-to-end fully automatic approach based on Mask R-CNN for instance segmentation and classification of glomeruli. We also compared the results obtained with a baseline based on Faster R-CNN, which only allows detection at bounding boxes level. With respect to the existing literature, we improved the Mask R-CNN approach in sliding window contexts, by employing a variant of the Non-Maximum Suppression (NMS) algorithm, which we called Non-Maximum-Area Suppression (NMAS). The obtained results are very promising, leading to improvements over existing literature. The baseline Faster R-CNN-based approach obtained an F-Measure of 0.904 and 0.667 for non-sclerotic and sclerotic glomeruli, respectively. The Mask R-CNN approach has a significant improvement over the baseline, obtaining an F-Measure of 0.925 and 0.777 for non-sclerotic and sclerotic glomeruli, respectively. The proposed method is very promising for the instance segmentation and classification of glomeruli, and allows to make a robust evaluation of global glomerulosclerosis. We also compared Karpinski score obtained with our algorithm to that obtained with pathologists’ annotations to show the soundness of the proposed workflow from a clinical point of view.

scholarly journals InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dominik Jens Elias Waibel ◽  
Sayedali Shetab Boushehri ◽  
Carsten Marr
Keyword(s):  
Image Processing ◽  
Deep Learning ◽  
Specific Problem ◽  
State Of The Art ◽  
Image Data ◽  
Semantic Segmentation ◽  
Parameter Tuning ◽  
Cellular Processes ◽  
Minimal Effort ◽  
Instance Segmentation

Abstract Background Deep learning contributes to uncovering molecular and cellular processes with highly performant algorithms. Convolutional neural networks have become the state-of-the-art tool to provide accurate and fast image data processing. However, published algorithms mostly solve only one specific problem and they typically require a considerable coding effort and machine learning background for their application. Results We have thus developed InstantDL, a deep learning pipeline for four common image processing tasks: semantic segmentation, instance segmentation, pixel-wise regression and classification. InstantDL enables researchers with a basic computational background to apply debugged and benchmarked state-of-the-art deep learning algorithms to their own data with minimal effort. To make the pipeline robust, we have automated and standardized workflows and extensively tested it in different scenarios. Moreover, it allows assessing the uncertainty of predictions. We have benchmarked InstantDL on seven publicly available datasets achieving competitive performance without any parameter tuning. For customization of the pipeline to specific tasks, all code is easily accessible and well documented. Conclusions With InstantDL, we hope to empower biomedical researchers to conduct reproducible image processing with a convenient and easy-to-use pipeline.

Introducing AIDE: a Software Suite for Annotating Images with Deep and Active Learning Assistance

2021 ◽  
Author(s):  
Benjamin Kellenberger ◽  
Devis Tuia ◽  
Dan Morris
Keyword(s):  
Deep Learning ◽  
Active Learning ◽  
Expert Knowledge ◽  
Semantic Segmentation ◽  
Third Party ◽  
Learning Models ◽  
Web Browser ◽  
Web Based ◽  
Model Training ◽  
Bounding Boxes

<p>Ecological research like wildlife censuses increasingly relies on data on the scale of Terabytes. For example, modern camera trap datasets contain millions of images that require prohibitive amounts of manual labour to be annotated with species, bounding boxes, and the like. Machine learning, especially deep learning [3], could greatly accelerate this task through automated predictions, but involves expansive coding and expert knowledge.</p><p>In this abstract we present AIDE, the Annotation Interface for Data-driven Ecology [2]. In a first instance, AIDE is a web-based annotation suite for image labelling with support for concurrent access and scalability, up to the cloud. In a second instance, it tightly integrates deep learning models into the annotation process through active learning [7], where models learn from user-provided labels and in turn select the most relevant images for review from the large pool of unlabelled ones (Fig. 1). The result is a system where users only need to label what is required, which saves time and decreases errors due to fatigue.</p><p><img src="https://contentmanager.copernicus.org/fileStorageProxy.php?f=gnp.0402be60f60062057601161/sdaolpUECMynit/12UGE&app=m&a=0&c=131251398e575ac9974634bd0861fadc&ct=x&pn=gnp.elif&d=1" alt=""></p><p><em>Fig. 1: AIDE offers concurrent web image labelling support and uses annotations and deep learning models in an active learning loop.</em></p><p>AIDE includes a comprehensive set of built-in models, such as ResNet [1] for image classification, Faster R-CNN [5] and RetinaNet [4] for object detection, and U-Net [6] for semantic segmentation. All models can be customised and used without having to write a single line of code. Furthermore, AIDE accepts any third-party model with minimal implementation requirements. To complete the package, AIDE offers both user annotation and model prediction evaluation, access control, customisable model training, and more, all through the web browser.</p><p>AIDE is fully open source and available under https://github.com/microsoft/aerial_wildlife_detection.</p><p> </p><p><strong>References</strong></p>

scholarly journals FUSION OF FEATURE BASED AND DEEP LEARNING METHODS FOR CLASSIFICATION OF MMS POINT CLOUDS

2019 ◽  
Vol XLII-2/W16 ◽  
pp. 235-242 ◽  
Author(s):  
D. Tosic ◽  
S. Tuttas ◽  
L. Hoegner ◽  
U. Stilla
Keyword(s):  
Deep Learning ◽  
Point Cloud ◽  
Semantic Segmentation ◽  
Point Clouds ◽  
Local Geometry ◽  
Learning Approach ◽  
Semantic Classification ◽  
Feature Based ◽  
Urban Scene

<p><strong>Abstract.</strong> This work proposes an approach for semantic classification of an outdoor-scene point cloud acquired with a high precision Mobile Mapping System (MMS), with major goal to contribute to the automatic creation of High Definition (HD) Maps. The automatic point labeling is achieved by utilizing the combination of a feature-based approach for semantic classification of point clouds and a deep learning approach for semantic segmentation of images. Both, point cloud data, as well as the data from a multi-camera system are used for gaining spatial information in an urban scene. Two types of classification applied for this task are: 1) Feature-based approach, in which the point cloud is organized into a supervoxel structure for capturing geometric characteristics of points. Several geometric features are then extracted for appropriate representation of the local geometry, followed by removing the effect of local tendency for each supervoxel to enhance the distinction between similar structures. And lastly, the Random Forests (RF) algorithm is applied in the classification phase, for assigning labels to supervoxels and therefore to points within them. 2) The deep learning approach is employed for semantic segmentation of MMS images of the same scene. To achieve this, an implementation of Pyramid Scene Parsing Network is used. Resulting segmented images with each pixel containing a class label are then projected onto the point cloud, enabling label assignment for each point. At the end, experiment results are presented from a complex urban scene and the performance of this method is evaluated on a manually labeled dataset, for the deep learning and feature-based classification individually, as well as for the result of the labels fusion. The achieved overall accuracy with fusioned output is 0.87 on the final test set, which significantly outperforms the results of individual methods on the same point cloud. The labeled data is published on the TUM-PF Semantic-Labeling-Benchmark.</p>

scholarly journals AUTOMATED MARINE OIL SPILL DETECTION USING DEEP LEARNING INSTANCE SEGMENTATION MODEL

2020 ◽  
Vol XLIII-B3-2020 ◽  
pp. 1271-1276
Author(s):  
S. T. Yekeen ◽  
A.-L. Balogun
Keyword(s):  
Deep Learning ◽  
Oil Spill ◽  
Semantic Segmentation ◽  
Learning Models ◽  
Marine Oil ◽  
Conventional Machine ◽  
Feature Pyramid ◽  
Model Training ◽  
Instance Segmentation ◽  
Better Than

Abstract. This study developed a novel deep learning oil spill instance segmentation model using Mask-Region-based Convolutional Neural Network (Mask R-CNN) model which is a state-of-the-art computer vision model. A total of 2882 imageries containing oil spill, look-alike, ship, and land area after conducting different pre-processing activities were acquired. These images were subsequently sub-divided into 88% training and 12% for testing, equating to 2530 and 352 images respectively. The model training was conducted using transfer learning on a pre-trained ResNet 101 with COCO data as a backbone in combination with Feature Pyramid Network (FPN) architecture for the extraction of features at 30 epochs with 0.001 learning rate. The model’s performance was evaluated using precision, recall, and F1-measure which shows a higher performance than other existing models with value of 0.964, 0.969 and 0.968 respectively. As a specialized task, the study concluded that the developed deep learning instance segmentation model (Mask R-CNN) performs better than conventional machine learning models and semantic segmentation deep learning models in detection and segmentation of marine oil spill.

scholarly journals HistoFlow: Label-Efficient and Interactive Deep Learning Cell Analysis

2020 ◽  
Author(s):  
Tim Henning ◽  
Benjamin Bergner ◽  
Christoph Lippert
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
User Interface ◽  
Network Architecture ◽  
Training Data ◽  
Cell Segmentation ◽  
Annotation Tool ◽  
Cell Analysis ◽  
Instance Segmentation

Instance segmentation is a common task in quantitative cell analysis. While there are many approaches doing this using machine learning, typically, the training process requires a large amount of manually annotated data. We present HistoFlow, a software for annotation-efficient training of deep learning models for cell segmentation and analysis with an interactive user interface.It provides an assisted annotation tool to quickly draw and correct cell boundaries and use biomarkers as weak annotations. It also enables the user to create artificial training data to lower the labeling effort. We employ a universal U-Net neural network architecture that allows accurate instance segmentation and the classification of phenotypes in only a single pass of the network. Transfer learning is available through the user interface to adapt trained models to new tissue types.We demonstrate HistoFlow for fluorescence breast cancer images. The models trained using only artificial data perform comparably to those trained with time-consuming manual annotations. They outperform traditional cell segmentation algorithms and match state-of-the-art machine learning approaches. A user test shows that cells can be annotated six times faster than without the assistance of our annotation tool. Extending a segmentation model for classification of epithelial cells can be done using only 50 to 1500 annotations.Our results show that, unlike previous assumptions, it is possible to interactively train a deep learning model in a matter of minutes without many manual annotations.

scholarly journals Semantic Segmentation Framework for Glomeruli Detection and Classification in Kidney Histological Sections

Electronics ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 503 ◽  
Author(s):  
Nicola Altini ◽  
Giacomo Donato Cascarano ◽  
Antonio Brunetti ◽  
Francescomaria Marino ◽  
Maria Teresa Rocchetti ◽  
...  
Keyword(s):  
High Performance ◽  
Evaluation Process ◽  
Semantic Segmentation ◽  
University Hospital ◽  
Detection Level ◽  
Cad System ◽  
Proposed Model ◽  
Segmentation Framework ◽  
Global Glomerulosclerosis ◽  
Aided Diagnosis

The evaluation of kidney biopsies performed by expert pathologists is a crucial process for assessing if a kidney is eligible for transplantation. In this evaluation process, an important step consists of the quantification of global glomerulosclerosis, which is the ratio between sclerotic glomeruli and the overall number of glomeruli. Since there is a shortage of organs available for transplantation, a quick and accurate assessment of global glomerulosclerosis is essential for retaining the largest number of eligible kidneys. In the present paper, the authors introduce a Computer-Aided Diagnosis (CAD) system to assess global glomerulosclerosis. The proposed tool is based on Convolutional Neural Networks (CNNs). In particular, the authors considered approaches based on Semantic Segmentation networks, such as SegNet and DeepLab v3+. The dataset has been provided by the Department of Emergency and Organ Transplantations (DETO) of Bari University Hospital, and it is composed of 26 kidney biopsies coming from 19 donors. The dataset contains 2344 non-sclerotic glomeruli and 428 sclerotic glomeruli. The proposed model consents to achieve promising results in the task of automatically detecting and classifying glomeruli, thus easing the burden of pathologists. We get high performance both at pixel-level, achieving mean F-score higher than 0.81, and Weighted Intersection over Union (IoU) higher than 0.97 for both SegNet and Deeplab v3+ approaches, and at object detection level, achieving 0.924 as best F-score for non-sclerotic glomeruli and 0.730 as best F-score for sclerotic glomeruli.

scholarly journals Evaluation of deep learning algorithms for semantic segmentation of car parts

2021 ◽  
Author(s):  
Kitsuchart Pasupa ◽  
Phongsathorn Kittiworapanya ◽  
Napasin Hongngern ◽  
Kuntpong Woraratpanya
Keyword(s):  
Deep Learning ◽  
Evaluation System ◽  
Learning Algorithms ◽  
Weather Conditions ◽  
Semantic Segmentation ◽  
Smart Device ◽  
Data Set ◽  
Basic Part ◽  
Left And Right ◽  
Instance Segmentation

AbstractEvaluation of car damages from an accident is one of the most important processes in the car insurance business. Currently, it still needs a manual examination of every basic part. It is expected that a smart device will be able to do this evaluation more efficiently in the future. In this study, we evaluated and compared five deep learning algorithms for semantic segmentation of car parts. The baseline reference algorithm was Mask R-CNN, and the other algorithms were HTC, CBNet, PANet, and GCNet. Runs of instance segmentation were conducted with those five algorithms. HTC with ResNet-50 was the best algorithm for instance segmentation on various kinds of cars such as sedans, trucks, and SUVs. It achieved a mean average precision at 55.2 on our original data set, that assigned different labels to the left and right sides and 59.1 when a single label was assigned to both sides. In addition, the models from every algorithm were tested for robustness, by running them on images of parts, in a real environment with various weather conditions, including snow, frost, fog and various lighting conditions. GCNet was the most robust; it achieved a mean performance under corruption, mPC = 35.2, and a relative degradation of performance on corrupted data, compared to clean data (rPC), of 64.4%, when left and right sides were assigned different labels, and mPC = 38.1 and rPC = $$69.6\%$$ 69.6 % when left- and right-side parts were considered the same part. The findings from this study may directly benefit developers of automated car damage evaluation system in their quest for the best design.

scholarly journals InstantDL - An easy-to-use deep learning pipeline for image segmentation and classification

2020 ◽  
Author(s):  
Dominik Waibel ◽  
Sayedali Shetab Boushehri ◽  
Carsten Marr
Keyword(s):  
Deep Learning ◽  
Specific Problem ◽  
State Of The Art ◽  
Image Data ◽  
Semantic Segmentation ◽  
Parameter Tuning ◽  
Biomedical Image ◽  
Cellular Processes ◽  
Minimal Effort ◽  
Instance Segmentation

AbstractMotivationDeep learning contributes to uncovering and understanding molecular and cellular processes with highly performant image computing algorithms. Convolutional neural networks have become the state-of-the-art tool to provide accurate, consistent and fast data processing. However, published algorithms mostly solve only one specific problem and they often require expert skills and a considerable computer science and machine learning background for application.ResultsWe have thus developed a deep learning pipeline called InstantDL for four common image processing tasks: semantic segmentation, instance segmentation, pixel-wise regression and classification. InstantDL enables experts and non-experts to apply state-of-the-art deep learning algorithms to biomedical image data with minimal effort. To make the pipeline robust, we have automated and standardized workflows and extensively tested it in different scenarios. Moreover, it allows to assess the uncertainty of predictions. We have benchmarked InstantDL on seven publicly available datasets achieving competitive performance without any parameter tuning. For customization of the pipeline to specific tasks, all code is easily accessible.Availability and ImplementationInstantDL is available under the terms of MIT licence. It can be found on GitHub: https://github.com/marrlab/[email protected]

scholarly journals Convolutional Neural Network-Based Instance Segmentation Algorithm to Acquire Quantitative Criteria of Early Mouse Development

2018 ◽  
Author(s):  
Yuta Tokuoka ◽  
Takahiro G Yamada ◽  
Noriko F Hiroi ◽  
Tetsuya J Kobayashi ◽  
Kazuo Yamagata ◽  
...  
Keyword(s):  
Neural Network ◽  
Image Processing ◽  
Deep Learning ◽  
Three Dimensional ◽  
Semantic Segmentation ◽  
Critical Issue ◽  
Segmentation Algorithm ◽  
Embryonic Cells ◽  
Mouse Development ◽  
Instance Segmentation

AbstractIn embryology, image processing methods such as segmentation are applied to acquiring quantitative criteria from time-series three-dimensional microscopic images. When used to segment cells or intracellular organelles, several current deep learning techniques outperform traditional image processing algorithms. However, segmentation algorithms still have unsolved problems, especially in bioimage processing. The most critical issue is that the existing deep learning-based algorithms for bioimages can perform only semantic segmentation, which distinguishes whether a pixel is within an object (for example, nucleus) or not. In this study, we implemented a novel segmentation algorithm, based on deep learning, which segments each nucleus and adds different labels to the detected objects. This segmentation algorithm is called instance segmentation. Our instance segmentation algorithm, implemented as a neural network, which we named QCA Net, substantially outperformed 3D U-Net, which is the best semantic segmentation algorithm that uses deep learning. Using QCA Net, we quantified the nuclear number, volume, surface area, and center of gravity coordinates during the development of mouse embryos. In particular, QCA Net distinguished nuclei of embryonic cells from those of polar bodies formed in meiosis. We consider that QCA Net can greatly contribute to bioimage segmentation in embryology by generating quantitative criteria from segmented images.

scholarly journals Automating classification of osteoarthritis according to Kellgren-Lawrence in the knee using deep learning in an unfiltered adult population

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Simon Olsson ◽  
Ehsan Akbarian ◽  
Anna Lind ◽  
Ali Sharif Razavian ◽  
Max Gordon
Keyword(s):  
Deep Learning ◽  
Knee Osteoarthritis ◽  
Adult Population ◽  
Weight Bearing ◽  
Correct Diagnosis ◽  
University Hospital ◽  
Knee Oa ◽  
Orthopedic Surgeons ◽  
Visual Disturbances

Abstract Background Prevalence for knee osteoarthritis is rising in both Sweden and globally due to increased age and obesity in the population. This has subsequently led to an increasing demand for knee arthroplasties. Correct diagnosis and classification of a knee osteoarthritis (OA) are therefore of a great interest in following-up and planning for either conservative or operative management. Most orthopedic surgeons rely on standard weight bearing radiographs of the knee. Improving the reliability and reproducibility of these interpretations could thus be hugely beneficial. Recently, deep learning which is a form of artificial intelligence (AI), has been showing promising results in interpreting radiographic images. In this study, we aim to evaluate how well an AI can classify the severity of knee OA, using entire image series and not excluding common visual disturbances such as an implant, cast and non-degenerative pathologies. Methods We selected 6103 radiographic exams of the knee taken at Danderyd University Hospital between the years 2002-2016 and manually categorized them according to the Kellgren & Lawrence grading scale (KL). We then trained a convolutional neural network (CNN) of ResNet architecture using PyTorch. We evaluated the results against a test set of 300 exams that had been reviewed independently by two senior orthopedic surgeons who settled eventual interobserver disagreements through consensus sessions. Results The CNN yielded an overall AUC of more than 0.87 for all KL grades except KL grade 2, which yielded an AUC of 0.8 and a mean AUC of 0.92. When merging adjacent KL grades, all but one group showed near perfect results with AUC > 0.95 indicating excellent performance. Conclusion We have found that we could teach a CNN to correctly diagnose and classify the severity of knee OA using the KL grading system without cleaning the input data from major visual disturbances such as implants and other pathologies.

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