scholarly journals DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation

2020 ◽  
Author(s):  
Ilya Belevich ◽  
Eija Jokitalo
Keyword(s):  
Deep Learning ◽  
Open Source ◽  
Open Source Software ◽  
Light And Electron Microscopy ◽  
Learning Approaches ◽  
Learning Network ◽  
Deep Learning Network ◽  
User Friendly ◽  
2D And 3D ◽  
Biological Image

AbstractDeep learning approaches are highly sought after solutions for coping with large amounts of collected datasets and are expected to become an essential part of imaging workflows. However, in most cases, deep learning is still considered as a complex task that only image analysis experts can master. DeepMIB addresses this problem and provides the community with a user-friendly and open-source tool to train convolutional neural networks and apply them to segment 2D and 3D light and electron microscopy datasets.

scholarly journals DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation

2021 ◽  
Vol 17 (3) ◽  
pp. e1008374
Author(s):  
Ilya Belevich ◽  
Eija Jokitalo
Keyword(s):  
Image Segmentation ◽  
Deep Learning ◽  
Open Source ◽  
Open Source Software ◽  
Learning Network ◽  
Matlab Code ◽  
Deep Learning Network ◽  
User Friendly ◽  
2D And 3D ◽  
Biological Image

We present DeepMIB, a new software package that is capable of training convolutional neural networks for segmentation of multidimensional microscopy datasets on any workstation. We demonstrate its successful application for segmentation of 2D and 3D electron and multicolor light microscopy datasets with isotropic and anisotropic voxels. We distribute DeepMIB as both an open-source multi-platform Matlab code and as compiled standalone application for Windows, MacOS and Linux. It comes in a single package that is simple to install and use as it does not require knowledge of programming. DeepMIB is suitable for everyone interested of bringing a power of deep learning into own image segmentation workflows.

scholarly journals Multi-Person Pose Estimation using an Orientation and Occlusion Aware Deep Learning Network

Sensors ◽  
2020 ◽  
Vol 20 (6) ◽  
pp. 1593 ◽  
Author(s):  
Yanlei Gu ◽  
Huiyang Zhang ◽  
Shunsuke Kamijo
Keyword(s):  
Deep Learning ◽  
Pose Estimation ◽  
Body Orientation ◽  
Learning Approaches ◽  
The Public ◽  
Learning Network ◽  
Proposed Model ◽  
Body Boundary ◽  
Public Dataset ◽  
Deep Learning Network

Image based human behavior and activity understanding has been a hot topic in the field of computer vision and multimedia. As an important part, skeleton estimation, which is also called pose estimation, has attracted lots of interests. For pose estimation, most of the deep learning approaches mainly focus on the joint feature. However, the joint feature is not sufficient, especially when the image includes multi-person and the pose is occluded or not fully visible. This paper proposes a novel multi-task framework for the multi-person pose estimation. The proposed framework is developed based on Mask Region-based Convolutional Neural Networks (R-CNN) and extended to integrate the joint feature, body boundary, body orientation and occlusion condition together. In order to further improve the performance of the multi-person pose estimation, this paper proposes to organize the different information in serial multi-task models instead of the widely used parallel multi-task network. The proposed models are trained on the public dataset Common Objects in Context (COCO), which is further augmented by ground truths of body orientation and mutual-occlusion mask. Experiments demonstrate the performance of the proposed method for multi-person pose estimation and body orientation estimation. The proposed method can detect 84.6% of the Percentage of Correct Keypoints (PCK) and has an 83.7% Correct Detection Rate (CDR). Comparisons further illustrate the proposed model can reduce the over-detection compared with other methods.

Forecasting Monthly Rainfall using Bio-Inspired Artificial Algae Deep Learning Network

2021 ◽  
Author(s):  
A. Kala ◽  
S. Ganesh Vaidyanathan
Keyword(s):  
Deep Learning ◽  
Time Series Data ◽  
Short Term Memory ◽  
Monthly Rainfall ◽  
Series Data ◽  
Learning Approaches ◽  
Rainfall Forecasting ◽  
Data Set ◽  
Learning Network ◽  
Deep Learning Network

Rainfall forecasting is the most critical and challenging task because of its dependence on different climatic and weather parameters. Hence, robust and accurate rainfall forecasting models need to be created by applying various machine learning and deep learning approaches. Several automatic systems were created to predict the weather, but it depends on the type of weather pattern, season and location, which leads in maximizing the processing time. Therefore, in this work, significant artificial algae long short-term memory (LSTM) deep learning network is introduced to forecast the monthly rainfall. During this process, Homogeneous Indian Monthly Rainfall Data Set (1871–2016) is utilized to collect the rainfall information. The gathered information is computed with the help of an LSTM approach, which is able to process the time series data and predict the dependency between the data effectively. The most challenging phase of LSTM training process is finding optimal network parameters such as weight and bias. For obtaining the optimal parameters, one of the Meta heuristic bio-inspired algorithms called Artificial Algae Algorithm (AAA) is used. The forecasted rainfall for the testing dataset is compared with the existing models. The forecasted results exhibit superiority of our model over the state-of-the-art models for forecasting Indian Monsoon rainfall. The LSTM model combined with AAA predicts the monsoon from June–September accurately.

scholarly journals UAVs in rail damage image diagnostics supported by deep-learning networks

2021 ◽  
Vol 11 (1) ◽  
pp. 339-348
Author(s):  
Piotr Bojarczak ◽  
Piotr Lesiak
Keyword(s):  
Deep Learning ◽  
Head Width ◽  
Learning Networks ◽  
Image Brightness ◽  
Learning Network ◽  
Rail Head ◽  
Image Recording ◽  
Python Language ◽  
Deep Learning Network ◽  
Efficiency Rate

Abstract The article uses images from Unmanned Aerial Vehicles (UAVs) for rail diagnostics. The main advantage of such a solution compared to traditional surveys performed with measuring vehicles is the elimination of decreased train traffic. The authors, in the study, limited themselves to the diagnosis of hazardous split defects in rails. An algorithm has been proposed to detect them with an efficiency rate of about 81% for defects not less than 6.9% of the rail head width. It uses the FCN-8 deep-learning network, implemented in the Tensorflow environment, to extract the rail head by image segmentation. Using this type of network for segmentation increases the resistance of the algorithm to changes in the recorded rail image brightness. This is of fundamental importance in the case of variable conditions for image recording by UAVs. The detection of these defects in the rail head is performed using an algorithm in the Python language and the OpenCV library. To locate the defect, it uses the contour of a separate rail head together with a rectangle circumscribed around it. The use of UAVs together with artificial intelligence to detect split defects is an important element of novelty presented in this work.

scholarly journals BioECG: Improving ECG Biometrics with Deep Learning and Enhanced Datasets

2021 ◽  
Vol 11 (13) ◽  
pp. 5880
Author(s):  
Paloma Tirado-Martin ◽  
Raul Sanchez-Reillo
Keyword(s):  
Deep Learning ◽  
Temporal Variations ◽  
Physical Activities ◽  
Learning Tools ◽  
Biometric Recognition ◽  
Learning Network ◽  
Deep Learning Network ◽  
Electrocardiogram Ecg

Nowadays, Deep Learning tools have been widely applied in biometrics. Electrocardiogram (ECG) biometrics is not the exception. However, the algorithm performances rely heavily on a representative dataset for training. ECGs suffer constant temporal variations, and it is even more relevant to collect databases that can represent these conditions. Nonetheless, the restriction in database publications obstructs further research on this topic. This work was developed with the help of a database that represents potential scenarios in biometric recognition as data was acquired in different days, physical activities and positions. The classification was implemented with a Deep Learning network, BioECG, avoiding complex and time-consuming signal transformations. An exhaustive tuning was completed including variations in enrollment length, improving ECG verification for more complex and realistic biometric conditions. Finally, this work studied one-day and two-days enrollments and their effects. Two-days enrollments resulted in huge general improvements even when verification was accomplished with more unstable signals. EER was improved in 63% when including a change of position, up to almost 99% when visits were in a different day and up to 91% if the user experienced a heartbeat increase after exercise.

scholarly journals Method for Diagnosing the Bone Marrow Edema of Sacroiliac Joint in Patients with Axial Spondyloarthritis Using Magnetic Resonance Image Analysis Based on Deep Learning

Diagnostics ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1156
Author(s):  
Kang Hee Lee ◽  
Sang Tae Choi ◽  
Guen Young Lee ◽  
You Jung Ha ◽  
Sang-Il Choi
Keyword(s):  
Bone Marrow ◽  
Deep Learning ◽  
Bone Marrow Edema ◽  
Axial Spondyloarthritis ◽  
Mr Images ◽  
Sacroiliac Joints ◽  
Learning Network ◽  
Active Sacroiliitis ◽  
Deep Learning Network ◽  
Marrow Edema

Axial spondyloarthritis (axSpA) is a chronic inflammatory disease of the sacroiliac joints. In this study, we develop a method for detecting bone marrow edema by magnetic resonance (MR) imaging of the sacroiliac joints and a deep-learning network. A total of 815 MR images of the sacroiliac joints were obtained from 60 patients diagnosed with axSpA and 19 healthy subjects. Gadolinium-enhanced fat-suppressed T1-weighted oblique coronal images were used for deep learning. Active sacroiliitis was defined as bone marrow edema, and the following processes were performed: setting the region of interest (ROI) and normalizing it to a size suitable for input to a deep-learning network, determining bone marrow edema using a convolutional-neural-network-based deep-learning network for individual MR images, and determining sacroiliac arthritis in subject examinations based on the classification results of individual MR images. About 70% of the patients and normal subjects were randomly selected for the training dataset, and the remaining 30% formed the test dataset. This process was repeated five times to calculate the average classification rate of the five-fold sets. The gradient-weighted class activation mapping method was used to validate the classification results. In the performance analysis of the ResNet18-based classification network for individual MR images, use of the ROI showed excellent detection performance of bone marrow edema with 93.55 ± 2.19% accuracy, 92.87 ± 1.27% recall, and 94.69 ± 3.03% precision. The overall performance was additionally improved using a median filter to reflect the context information. Finally, active sacroiliitis was diagnosed in individual subjects with 96.06 ± 2.83% accuracy, 100% recall, and 94.84 ± 3.73% precision. This is a pilot study to diagnose bone marrow edema by deep learning based on MR images, and the results suggest that MR analysis using deep learning can be a useful complementary means for clinicians to diagnose bone marrow edema.

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