scholarly journals Exploring Flood Filling Networks for Instance Segmentation of XXL-Volumetric and Bulk Material CT Data

2020 ◽  
Vol 40 (1) ◽  
Author(s):  
Roland Gruber ◽  
Stefan Gerth ◽  
Joelle Claußen ◽  
Norbert Wörlein ◽  
Norman Uhlmann ◽  
...  
Keyword(s):  
Large Scale ◽  
Bulk Material ◽  
Automatic Segmentation ◽  
Image Data ◽  
Real Data ◽  
Specific Information ◽  
Volume Data ◽  
Beam Hardening ◽  
Exploration Process ◽  
Instance Segmentation

AbstractXXL-Computed Tomography (XXL-CT) is able to produce large scale volume datasets of scanned objects such as crash tested cars, sea and aircraft containers or cultural heritage objects. The acquired image data consists of volumes of up to and above $$\hbox {10,000}^{3}$$ 10,000 3 voxels which can relate up to many terabytes in file size and can contain multiple 10,000 of different entities of depicted objects. In order to extract specific information about these entities from the scanned objects in such vast datasets, segmentation or delineation of these parts is necessary. Due to unknown and varying properties (shapes, densities, materials, compositions) of these objects, as well as interfering acquisition artefacts, classical (automatic) segmentation is usually not feasible. Contrarily, a complete manual delineation is error-prone and time-consuming, and can only be performed by trained and experienced personnel. Hence, an interactive and partial segmentation of so-called “chunks” into tightly coupled assemblies or sub-assemblies may help the assessment, exploration and understanding of such large scale volume data. In order to assist users with such an (possibly interactive) instance segmentation for the data exploration process, we propose to utilize delineation algorithms with an approach derived from flood filling networks. We present primary results of a flood filling network implementation adapted to non-destructive testing applications based on large scale CT from various test objects, as well as real data of an airplane and describe the adaptions to this domain. Furthermore, we address and discuss segmentation challenges due to acquisition artefacts such as scattered radiation or beam hardening resulting in reduced data quality, which can severely impair the interactive segmentation results.

scholarly journals Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data

2019 ◽  
Author(s):  
Robert Krueger ◽  
Johanna Beyer ◽  
Won-Dong Jang ◽  
Nam Wook Kim ◽  
Artem Sokolov ◽  
...  
Keyword(s):  
Supervised Learning ◽  
Visual Analytics ◽  
Cancer Biology ◽  
Large Scale ◽  
Hierarchical Structures ◽  
Image Data ◽  
Automated Analysis ◽  
Cell Types ◽  
High Dimensional ◽  
Exploration Process

AbstractFacetto is a scalable visual analytics application that is used to discover single-cell phenotypes in high-dimensional multi-channel microscopy images of human tumors and tissues. Such images represent the cutting edge of digital histology and promise to revolutionize how diseases such as cancer are studied, diagnosed, and treated. Highly multiplexed tissue images are complex, comprising 109or more pixels, 60-plus channels, and millions of individual cells. This makes manual analysis challenging and error-prone. Existing automated approaches are also inadequate, in large part, because they are unable to effectively exploit the deep knowledge of human tissue biology available to anatomic pathologists. To overcome these challenges, Facetto enables a semi-automated analysis of cell types and states. It integrates unsupervised and supervised learning into the image and feature exploration process and offers tools for analytical provenance. Experts can cluster the data to discover new types of cancer and immune cells and use clustering results to train a convolutional neural network that classifies new cells accordingly. Likewise, the output of classifiers can be clustered to discover aggregate patterns and phenotype subsets. We also introduce a new hierarchical approach to keep track of analysis steps and data subsets created by users; this assists in the identification of cell types. Users can build phenotype trees and interact with the resulting hierarchical structures of both high-dimensional feature and image spaces. We report on use-cases in which domain scientists explore various large-scale fluorescence imaging datasets. We demonstrate how Facetto assists users in steering the clustering and classification process, inspecting analysis results, and gaining new scientific insights into cancer biology.

Unmixing of large-scale hyperspectral data based on projected mini-batch gradient descent

2017 ◽  
Vol 15 (06) ◽  
pp. 1750059 ◽  
Author(s):  
Jing Li ◽  
Xiaorun Li ◽  
Liaoying Zhao
Keyword(s):  
Minimization Problem ◽  
Gradient Descent ◽  
Large Scale ◽  
Hyperspectral Image ◽  
Computational Cost ◽  
Nonnegative Matrix ◽  
Image Data ◽  
Real Data ◽  
Optimization Method ◽  
Hyperspectral Data

The minimization problem of reconstruction error over large hyperspectral image data is one of the most important problems in unsupervised hyperspectral unmixing. A variety of algorithms based on nonnegative matrix factorization (NMF) have been proposed in the literature to solve this minimization problem. One popular optimization method for NMF is the projected gradient descent (PGD). However, as the algorithm must compute the full gradient on the entire dataset at every iteration, the PGD suffers from high computational cost in the large-scale real hyperspectral image. In this paper, we try to alleviate this problem by introducing a mini-batch gradient descent-based algorithm, which has been widely used in large-scale machine learning. In our method, the endmember can be updated pixel set by pixel set while abundance can be updated band set by band set. Thus, the computational cost is lowered to a certain extent. The performance of the proposed algorithm is quantified in the experiment on synthetic and real data.

scholarly journals Large-Scale Road Network Congestion Pattern Analysis and Prediction Using Deep Convolutional Autoencoder

2021 ◽  
Vol 13 (9) ◽  
pp. 5108
Author(s):  
Navin Ranjan ◽  
Sovit Bhandari ◽  
Pervez Khan ◽  
Youn-Sik Hong ◽  
Hoon Kim
Keyword(s):  
Traffic Congestion ◽  
Network Architecture ◽  
Road Network ◽  
Large Scale ◽  
Pattern Analysis ◽  
Image Data ◽  
Urban Life ◽  
Prediction Algorithm ◽  
Rapid Urbanization ◽  
Convolutional Autoencoder

The transportation system, especially the road network, is the backbone of any modern economy. However, with rapid urbanization, the congestion level has surged drastically, causing a direct effect on the quality of urban life, the environment, and the economy. In this paper, we propose (i) an inexpensive and efficient Traffic Congestion Pattern Analysis algorithm based on Image Processing, which identifies the group of roads in a network that suffers from reoccurring congestion; (ii) deep neural network architecture, formed from Convolutional Autoencoder, which learns both spatial and temporal relationships from the sequence of image data to predict the city-wide grid congestion index. Our experiment shows that both algorithms are efficient because the pattern analysis is based on the basic operations of arithmetic, whereas the prediction algorithm outperforms two other deep neural networks (Convolutional Recurrent Autoencoder and ConvLSTM) in terms of large-scale traffic network prediction performance. A case study was conducted on the dataset from Seoul city.

scholarly journals NPU RGB+D Dataset and a Feature-Enhanced LSTM-DGCN Method for Action Recognition of Basketball Players

2021 ◽  
Vol 11 (10) ◽  
pp. 4426
Author(s):  
Chunyan Ma ◽  
Ji Fan ◽  
Jinghao Yao ◽  
Tao Zhang
Keyword(s):  
Action Recognition ◽  
Large Scale ◽  
Short Term Memory ◽  
Evaluation Criteria ◽  
Image Data ◽  
Basketball Player ◽  
Basketball Players ◽  
Convolutional Network ◽  
Atomic Actions ◽  
New Feature

Computer vision-based action recognition of basketball players in basketball training and competition has gradually become a research hotspot. However, owing to the complex technical action, diverse background, and limb occlusion, it remains a challenging task without effective solutions or public dataset benchmarks. In this study, we defined 32 kinds of atomic actions covering most of the complex actions for basketball players and built the dataset NPU RGB+D (a large scale dataset of basketball action recognition with RGB image data and Depth data captured in Northwestern Polytechnical University) for 12 kinds of actions of 10 professional basketball players with 2169 RGB+D videos and 75 thousand frames, including RGB frame sequences, depth maps, and skeleton coordinates. Through extracting the spatial features of the distances and angles between the joint points of basketball players, we created a new feature-enhanced skeleton-based method called LSTM-DGCN for basketball player action recognition based on the deep graph convolutional network (DGCN) and long short-term memory (LSTM) methods. Many advanced action recognition methods were evaluated on our dataset and compared with our proposed method. The experimental results show that the NPU RGB+D dataset is very competitive with the current action recognition algorithms and that our LSTM-DGCN outperforms the state-of-the-art action recognition methods in various evaluation criteria on our dataset. Our action classifications and this NPU RGB+D dataset are valuable for basketball player action recognition techniques. The feature-enhanced LSTM-DGCN has a more accurate action recognition effect, which improves the motion expression ability of the skeleton data.

scholarly journals BiPSim: a flexible and generic stochastic simulator for polymerization processes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Stephan Fischer ◽  
Marc Dinh ◽  
Vincent Henry ◽  
Philippe Robert ◽  
Anne Goelzer ◽  
...  
Keyword(s):  
Large Scale ◽  
Stochastic Simulation Algorithm ◽  
Specific Information ◽  
Whole Cell ◽  
Simulation Speed ◽  
Genome Wide ◽  
Cell Simulation ◽  
Stochastic Simulator ◽  
Modeling Formalisms ◽  
Stochastic Phenomena

AbstractDetailed whole-cell modeling requires an integration of heterogeneous cell processes having different modeling formalisms, for which whole-cell simulation could remain tractable. Here, we introduce BiPSim, an open-source stochastic simulator of template-based polymerization processes, such as replication, transcription and translation. BiPSim combines an efficient abstract representation of reactions and a constant-time implementation of the Gillespie’s Stochastic Simulation Algorithm (SSA) with respect to reactions, which makes it highly efficient to simulate large-scale polymerization processes stochastically. Moreover, multi-level descriptions of polymerization processes can be handled simultaneously, allowing the user to tune a trade-off between simulation speed and model granularity. We evaluated the performance of BiPSim by simulating genome-wide gene expression in bacteria for multiple levels of granularity. Finally, since no cell-type specific information is hard-coded in the simulator, models can easily be adapted to other organismal species. We expect that BiPSim should open new perspectives for the genome-wide simulation of stochastic phenomena in biology.

scholarly journals Constructing Large-Scale Genetic Maps Using an Evolutionary Strategy Algorithm

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2269-2282
Author(s):  
D Mester ◽  
Y Ronin ◽  
D Minkov ◽  
E Nevo ◽  
A Korol
Keyword(s):  
Discrete Optimization ◽  
High Performance ◽  
Large Scale ◽  
Simulated Data ◽  
Real Data ◽  
Genetic Maps ◽  
Chromosome 1 ◽  
Evolutionary Strategy ◽  
Group A ◽  
The One

Abstract This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with ∼50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology.

scholarly journals A Matheuristic Approach Combining Local Search and Mathematical Programming

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Carolina Lagos ◽  
Guillermo Guerrero ◽  
Enrique Cabrera ◽  
Stefanie Niklander ◽  
Franklin Johnson ◽  
...  
Keyword(s):  
Mathematical Programming ◽  
Local Search ◽  
Large Scale ◽  
Search Algorithm ◽  
Facility Location Problem ◽  
Specific Information ◽  
Local Search Algorithm ◽  
Capacitated Facility Location Problem ◽  
Capacitated Facility Location ◽  
Installation Cost

A novel matheuristic approach is presented and tested on a well-known optimisation problem, namely, capacitated facility location problem (CFLP). The algorithm combines local search and mathematical programming. While the local search algorithm is used to select a subset of promising facilities, mathematical programming strategies are used to solve the subproblem to optimality. Proposed local search is influenced by instance-specific information such as installation cost and the distance between customers and facilities. The algorithm is tested on large instances of the CFLP, where neither local search nor mathematical programming is able to find good quality solutions within acceptable computational times. Our approach is shown to be a very competitive alternative to solve large-scale instances for the CFLP.

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.

scholarly journals Towards pixel-to-pixel deep nucleus detection in microscopy images

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Fuyong Xing ◽  
Yuanpu Xie ◽  
Xiaoshuang Shi ◽  
Pingjun Chen ◽  
Zizhao Zhang ◽  
...  
Keyword(s):  
Neural Networks ◽  
Large Scale ◽  
Deep Neural Networks ◽  
Image Data ◽  
Fine Tuning ◽  
Cell Detection ◽  
Imaging Protocol ◽  
Microscopy Image ◽  
Microscopy Images ◽  
Target Data

Abstract Background Nucleus or cell detection is a fundamental task in microscopy image analysis and supports many other quantitative studies such as object counting, segmentation, tracking, etc. Deep neural networks are emerging as a powerful tool for biomedical image computing; in particular, convolutional neural networks have been widely applied to nucleus/cell detection in microscopy images. However, almost all models are tailored for specific datasets and their applicability to other microscopy image data remains unknown. Some existing studies casually learn and evaluate deep neural networks on multiple microscopy datasets, but there are still several critical, open questions to be addressed. Results We analyze the applicability of deep models specifically for nucleus detection across a wide variety of microscopy image data. More specifically, we present a fully convolutional network-based regression model and extensively evaluate it on large-scale digital pathology and microscopy image datasets, which consist of 23 organs (or cancer diseases) and come from multiple institutions. We demonstrate that for a specific target dataset, training with images from the same types of organs might be usually necessary for nucleus detection. Although the images can be visually similar due to the same staining technique and imaging protocol, deep models learned with images from different organs might not deliver desirable results and would require model fine-tuning to be on a par with those trained with target data. We also observe that training with a mixture of target and other/non-target data does not always mean a higher accuracy of nucleus detection, and it might require proper data manipulation during model training to achieve good performance. Conclusions We conduct a systematic case study on deep models for nucleus detection in a wide variety of microscopy images, aiming to address several important but previously understudied questions. We present and extensively evaluate an end-to-end, pixel-to-pixel fully convolutional regression network and report a few significant findings, some of which might have not been reported in previous studies. The model performance analysis and observations would be helpful to nucleus detection in microscopy images.

scholarly journals Meta-Descent for Online, Continual Prediction

2019 ◽  
Vol 33 ◽  
pp. 3943-3950
Author(s):  
Andrew Jacobsen ◽  
Matthew Schlegel ◽  
Cameron Linke ◽  
Thomas Degris ◽  
Adam White ◽  
...  
Keyword(s):  
Gradient Descent ◽  
Large Scale ◽  
Time Series Prediction ◽  
Real Data ◽  
Second Order ◽  
Stochastic Gradient Descent ◽  
Step Size ◽  
Vector Approximation ◽  
Prediction Problems ◽  
Stationary Problems

This paper investigates different vector step-size adaptation approaches for non-stationary online, continual prediction problems. Vanilla stochastic gradient descent can be considerably improved by scaling the update with a vector of appropriately chosen step-sizes. Many methods, including AdaGrad, RMSProp, and AMSGrad, keep statistics about the learning process to approximate a second order update—a vector approximation of the inverse Hessian. Another family of approaches use meta-gradient descent to adapt the stepsize parameters to minimize prediction error. These metadescent strategies are promising for non-stationary problems, but have not been as extensively explored as quasi-second order methods. We first derive a general, incremental metadescent algorithm, called AdaGain, designed to be applicable to a much broader range of algorithms, including those with semi-gradient updates or even those with accelerations, such as RMSProp. We provide an empirical comparison of methods from both families. We conclude that methods from both families can perform well, but in non-stationary prediction problems the meta-descent methods exhibit advantages. Our method is particularly robust across several prediction problems, and is competitive with the state-of-the-art method on a large-scale, time-series prediction problem on real data from a mobile robot.

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