scholarly journals Deep-learning-based flexible pipeline for segmenting and tracking cells in 3D image time series for whole brain imaging

2018 ◽  
Author(s):  
Chentao Wen ◽  
Takuya Miura ◽  
Yukako Fujie ◽  
Takayuki Teramoto ◽  
Takeshi Ishihara ◽  
...  
Keyword(s):  
Deep Learning ◽  
Brain Imaging ◽  
Data Augmentation ◽  
Sampling Rate ◽  
Artificial Noise ◽  
3D Image ◽  
Whole Brain ◽  
Registration Method ◽  
Point Set Registration ◽  
Image Series

AbstractThe brain is a complex system that operates based on coordinated neuronal activities. Brain-wide cellular calcium imaging techniques have quickly advanced in recent years and become powerful tools for understanding the neuronal activities of small animal models. The whole brain imaging generally requires to extract the neuronal activities from three-dimensional (3D) image series. Unfortunately, the 3D image series are obtained under imaging conditions different among laboratories and extracting neuronal activities from the data requires multiple processes. Therefore researchers need to develop their own software, which has prevented the application of whole-brain imaging experiments in more laboratories. Here, we combined traditional image processing techniques with the powerful deep-learning method which can be flexibly modified to fit 3D image data in the nematode Caenorhabditis elegans obtained under different conditions. We first trained the 3D U-net deep network to classify each pixel into cell and non-cell categories. Cells merged as a whole region were further separated into individual cells by watershed segmentation. The cells were then tracked in 3D space over time with the combination of a feedforward network and a point set registration method to use local and global relative positions of the cells, respectively. Remarkably, one manually annotated 3D image combined with data augmentation was sufficient for training the deep networks to obtain satisfactory tracking results. Our method correctly tracked more than 98% of neurons in three different image datasets and successfully extracted brain-wide neuronal activities. Our method worked well even when the sampling rate was reduced: 86% correct in case 4/5 frames were removed, and when artificial noise was added into the raw images: 91% correct in case 35 times of background-level noise was added. Our results proved that deep learning is widely applicable to different datasets and can help us in establishing a flexible pipeline for extracting whole brain activities.

scholarly journals Deep-learning-based whole-brain imaging at single-neuron resolution

2020 ◽  
Vol 11 (7) ◽  
pp. 3567
Author(s):  
Kefu Ning ◽  
Xiaoyu Zhang ◽  
Xuefei Gao ◽  
Tao Jiang ◽  
He Wang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Brain Imaging ◽  
Single Neuron ◽  
Whole Brain

Deep-learning-based whole-brain imaging at single-neuron resolution

2021 ◽  
Author(s):  
Kefu Ning ◽  
Xiaoyu Zhang ◽  
Xuefei Gao ◽  
Tao Jiang ◽  
He Wang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Brain Imaging ◽  
Single Neuron ◽  
Whole Brain

Levenshtein Augmentation Improves Performance of SMILES Based Deep-Learning Synthesis Prediction

2020 ◽  
Author(s):  
Dean Sumner ◽  
Jiazhen He ◽  
Amol Thakkar ◽  
Ola Engkvist ◽  
Esben Jannik Bjerrum
Keyword(s):  
Neural Networks ◽  
Pattern Recognition ◽  
Deep Learning ◽  
Recurrent Neural Networks ◽  
Data Augmentation ◽  
State Of The Art ◽  
Sequence Similarity ◽  
Learning Models ◽  
Underlying Network

<p>SMILES randomization, a form of data augmentation, has previously been shown to increase the performance of deep learning models compared to non-augmented baselines. Here, we propose a novel data augmentation method we call “Levenshtein augmentation” which considers local SMILES sub-sequence similarity between reactants and their respective products when creating training pairs. The performance of Levenshtein augmentation was tested using two state of the art models - transformer and sequence-to-sequence based recurrent neural networks with attention. Levenshtein augmentation demonstrated an increase performance over non-augmented, and conventionally SMILES randomization augmented data when used for training of baseline models. Furthermore, Levenshtein augmentation seemingly results in what we define as <i>attentional gain </i>– an enhancement in the pattern recognition capabilities of the underlying network to molecular motifs.</p>

A Deep Learning based Arabic Script Recognition System: Benchmark on KHAT

2020 ◽  
Vol 17 (3) ◽  
pp. 299-305 ◽  
Author(s):  
Riaz Ahmad ◽  
Saeeda Naz ◽  
Muhammad Afzal ◽  
Sheikh Rashid ◽  
Marcus Liwicki ◽  
...  
Keyword(s):  
Deep Learning ◽  
Character Recognition ◽  
Data Augmentation ◽  
Short Term Memory ◽  
Recognition System ◽  
Learning Approach ◽  
Arabic Text ◽  
Data Set ◽  
Processing Step ◽  
Handwritten Arabic

This paper presents a deep learning benchmark on a complex dataset known as KFUPM Handwritten Arabic TexT (KHATT). The KHATT data-set consists of complex patterns of handwritten Arabic text-lines. This paper contributes mainly in three aspects i.e., (1) pre-processing, (2) deep learning based approach, and (3) data-augmentation. The pre-processing step includes pruning of white extra spaces plus de-skewing the skewed text-lines. We deploy a deep learning approach based on Multi-Dimensional Long Short-Term Memory (MDLSTM) networks and Connectionist Temporal Classification (CTC). The MDLSTM has the advantage of scanning the Arabic text-lines in all directions (horizontal and vertical) to cover dots, diacritics, strokes and fine inflammation. The data-augmentation with a deep learning approach proves to achieve better and promising improvement in results by gaining 80.02% Character Recognition (CR) over 75.08% as baseline.

scholarly journals Application of Deep Learning in Integrated Pest Management: A Real-Time System for Detection and Diagnosis of Oilseed Rape Pests

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Yong He ◽  
Hong Zeng ◽  
Yangyang Fan ◽  
Shuaisheng Ji ◽  
Jianjian Wu
Keyword(s):  
Deep Learning ◽  
Integrated Pest Management ◽  
Pest Management ◽  
Real Time ◽  
Oilseed Rape ◽  
Data Augmentation ◽  
Low Cost ◽  
Response Speed ◽  
Original Model ◽  
Real Time System

In this paper, we proposed an approach to detect oilseed rape pests based on deep learning, which improves the mean average precision (mAP) to 77.14%; the result increased by 9.7% with the original model. We adopt this model to mobile platform to let every farmer able to use this program, which will diagnose pests in real time and provide suggestions on pest controlling. We designed an oilseed rape pest imaging database with 12 typical oilseed rape pests and compared the performance of five models, SSD w/Inception is chosen as the optimal model. Moreover, for the purpose of the high mAP, we have used data augmentation (DA) and added a dropout layer. The experiments are performed on the Android application we developed, and the result shows that our approach surpasses the original model obviously and is helpful for integrated pest management. This application has improved environmental adaptability, response speed, and accuracy by contrast with the past works and has the advantage of low cost and simple operation, which are suitable for the pest monitoring mission of drones and Internet of Things (IoT).

scholarly journals Chemical sectioning fluorescence tomography: high-throughput, high-contrast, multicolor, whole-brain imaging at subcellular resolution

Cell Reports ◽  
2021 ◽  
Vol 34 (5) ◽  
pp. 108709
Author(s):  
Xiaojun Wang ◽  
Hanqing Xiong ◽  
Yurong Liu ◽  
Tao Yang ◽  
Anan Li ◽  
...  
Keyword(s):  
Brain Imaging ◽  
High Throughput ◽  
High Contrast ◽  
Whole Brain ◽  
Fluorescence Tomography ◽  
Subcellular Resolution

scholarly journals Data augmentation for computed tomography angiography via synthetic image generation and neural domain adaptation

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Malte Seemann ◽  
Lennart Bargsten ◽  
Alexander Schlaefer
Keyword(s):  
Computed Tomography ◽  
Neural Networks ◽  
Deep Learning ◽  
Medical Imaging ◽  
Computed Tomography Angiography ◽  
Data Augmentation ◽  
Domain Adaptation ◽  
Synthetic Image ◽  
Wide Range ◽  
The Impact

AbstractDeep learning methods produce promising results when applied to a wide range of medical imaging tasks, including segmentation of artery lumen in computed tomography angiography (CTA) data. However, to perform sufficiently, neural networks have to be trained on large amounts of high quality annotated data. In the realm of medical imaging, annotations are not only quite scarce but also often not entirely reliable. To tackle both challenges, we developed a two-step approach for generating realistic synthetic CTA data for the purpose of data augmentation. In the first step moderately realistic images are generated in a purely numerical fashion. In the second step these images are improved by applying neural domain adaptation. We evaluated the impact of synthetic data on lumen segmentation via convolutional neural networks (CNNs) by comparing resulting performances. Improvements of up to 5% in terms of Dice coefficient and 20% for Hausdorff distance represent a proof of concept that the proposed augmentation procedure can be used to enhance deep learning-based segmentation for artery lumen in CTA images.

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