As-Built Inventory and Deformation Analysis of a High Rockfill Dam under Construction with Terrestrial Laser Scanning

The construction of large earth/rock fill dams, albeit its remarkable progress, still relies largely on past experiences. Therefore, a comprehensive yet dependable monitoring program is particularly beneficial for guiding the practice. However, conventional measurements can only produce limited discrete data. This paper exploits the potential of the terrestrial laser scanning (TLS) for an accurate inventory of as-built states of a concrete-faced rockfill dam under construction and for a full-field analysis of the 3D deformation pattern over its upstream face. For the former, a well-designed 3D geodetic system, with a particular consideration of the topography, promises a regulated acquisition of high-quality and blind-zone-free point cloud at field and also eases the cumbersome data registration process while maintaining its precision in house. For the latter, a problem-tailored processing pipeline is proposed for deformation extraction. Its core idea is to achieve a highly precise alignment of the point clouds with Iterative Closed Point algorithms from different epochs in datum areas that displays a featured, undeformed geometry at stable positions across epochs. Then, the alignment transformation matrix is applied to the point clouds of respective upstream face for each epoch, followed by pairwise comparisons of multiple adjusted point clouds for deformation evaluation. A processing pipeline is used to exploit the peal scene data redundancy of the GLQ dam acquired at six different epochs. Statistical analysis shows that satisfactory accuracy for deformation detection can be repeatably achieved, regardless of the scanner’s positioning uncertainties. The obtained 3D deformation patterns are characterised by three different zones: practically undeformed, outward and inward deformed zones. Their evolutions comply well with real construction stages and unique 3D valley topography. Abundant deformation results highlight the potential of TLS combined with the proposed data processing pipeline for cost-efficient monitoring of huge infrastructures compared to conventional labor-intense measurements.

Automatic Processing Pipeline for Collecting and Annotating Air-Traffic Voice Communication Data

This document describes our pipeline for automatic processing of ATCO pilot audio communication we developed as part of the ATCO2 project. So far, we collected two thousand hours of audio recordings that we either preprocessed for the transcribers or used for semi-supervised training. Both methods of using the collected data can further improve our pipeline by retraining our models. The proposed automatic processing pipeline is a cascade of many standalone components: (a) segmentation, (b) volume control, (c) signal-to-noise ratio filtering, (d) diarization, (e) ‘speech-to-text’ (ASR) module, (f) English language detection, (g) call-sign code recognition, (h) ATCO—pilot classification and (i) highlighting commands and values. The key component of the pipeline is a speech-to-text transcription system that has to be trained with real-world ATC data; otherwise, the performance is poor. In order to further improve speech-to-text performance, we apply both semi-supervised training with our recordings and the contextual adaptation that uses a list of plausible callsigns from surveillance data as auxiliary information. Downstream NLP/NLU tasks are important from an application point of view. These application tasks need accurate models operating on top of the real speech-to-text output; thus, there is a need for more data too. Creating ATC data is the main aspiration of the ATCO2 project. At the end of the project, the data will be packaged and distributed by ELDA.

An effective simulation- and measurement-based workflow for enhanced diagnostics in rhinology

Physics-based analyses have the potential to consolidate and substantiate medical diagnoses in rhinology. Such methods are frequently subject to intense investigations in research. However, they are not used in clinical applications, yet. One issue preventing their direct integration is that these methods are commonly developed as isolated solutions which do not consider the whole chain of data processing from initial medical to higher valued data. This manuscript presents a workflow that incorporates the whole data processing pipeline based on a environment. Therefore, medical image data are fully automatically pre-processed by machine learning algorithms. The resulting geometries employed for the simulations on high-performance computing systems reach an accuracy of up to 99.5% compared to manually segmented geometries. Additionally, the user is enabled to upload and visualize 4-phase rhinomanometry data. Subsequent analysis and visualization of the simulation outcome extend the results of standardized diagnostic methods by a physically sound interpretation. Along with a detailed presentation of the methodologies, the capabilities of the workflow are demonstrated by evaluating an exemplary medical case. The pipeline output is compared to 4-phase rhinomanometry data. The comparison underlines the functionality of the pipeline. However, it also illustrates the influence of mucosa swelling on the simulation.

A library for fMRI real-time processing systems in python (RTPSpy) with comprehensive online noise reduction, fast and accurate anatomical image processing, and online processing simulation

We introduce a python library for real-time fMRI (rtfMRI) data processing systems, Real-Time Processing System in python (RTPSpy), to provide building blocks for a custom rtfMRI application with extensive and advanced functionalities. RTPSpy is a library package including 1) a fast, comprehensive, and flexible online fMRI denoising pipeline comparable to offline processing, 2) utilities for fast and accurate anatomical image processing to define a target region on-site, 3) a simulation system of online fMRI processing to optimize a pipeline and target signal calculation, 4) interface to an external application for feedback presentation, and 5) a boilerplate graphical user interface (GUI) integrating operations with RTPSpy library. Since online fMRI data processing cannot be equivalent to offline, we discussed the limitations of online analysis and their solutions in the RTPSpy implementation. We developed a fast and accurate anatomical image processing script with fast tissue segmentation (FastSeg), image alignment, and spatial normalization, utilizing the FastSurfer, AFNI, and ANTs. We confirmed that the FastSeg output was comparable with FreeSurfer, and could complete all the anatomical image processing in a few minutes. Thanks to its highly modular architecture, RTPSpy can easily be used for a simulation analysis to optimize a processing pipeline and target signal calculation. We present a sample script for building a real-time processing pipeline and running a simulation using RTPSpy. The library also offers a simple signal exchange mechanism with an external application. An external application can receive a real-time neurofeedback signal from RTPSpy in a background thread with a few lines of script. While the main components of the RTPSpy are the library modules, we also provide a GUI class for easy access to the RTPSpy functions. The boilerplate GUI application provided with the package allows users to develop a customized rtfMRI application with minimum scripting labor. Finally, we discussed the limitations of the package regarding environment-specific implementations. We believe that RTPSpy is an attractive option for developing rtfMRI applications highly optimized for individual purposes. The package is available from GitHub (https://github.com/mamisaki/RTPSpy) with GPL3 license.

AutoMicroED: A semi-automated MicroED processing pipeline

Despite rapid adaptation of micro-electron diffraction (MicroED) for protein and small molecule structure determination to sub-angstrom resolution, the lack of automation tools for easy MicroED data processing remains a challenge for expanding to the broader scientific community. In particular, automation tools, which are novice user friendly, compatible with heterogenous datasets and can be run in unison with data collection to judge the quality of incoming data (similar to cryosparc LIVE for single particle cryoEM) do not exist. Here, we present AutoMicroED, a cohesive and semi-automatic MicroED data processing pipeline that runs through image conversion, indexing, integration and scaling of data, followed by merging of successful datasets that are pushed through phasing and final structure determination. AutoMicroED is compatible with both small molecule and protein datasets and creates a straightforward and reproducible method to solve single structures from pure samples, or multiple structures from mixed populations. The immediate feedback on data quality, data completeness and more parameters, aids users to identify whether they have collected enough data for their needs. Overall, AutoMicroED permits efficient structure elucidation for both novice and experienced users with comparable results to more laborious manual processing.

Quantitative Structural Analysis of Influenza Virus by Cryo-electron Tomography and Convolutional Neural Networks

Influenza viruses pose severe public health threats; they cause millions of infections and tens of thousands of deaths annually in the US. Influenza viruses are extensively pleomorphic, in both shape and size as well as organization of viral structural proteins. Analysis of influenza morphology and ultrastructure can help elucidate viral structure-function relationships as well as aid in therapeutics and vaccine development. While cryo-electron tomography (cryoET) can depict the 3D organization of pleomorphic influenza, the low signal-to-noise ratio inherent to cryoET and extensive viral heterogeneity have precluded detailed characterization of influenza viruses. In this report, we developed a cryoET processing pipeline leveraging convolutional neural networks (CNNs) to characterize the morphological architecture of the A/Puerto Rico/8/34 (H1N1) influenza strain. Our pipeline improved the throughput of cryoET analysis and accurately identified viral components within tomograms. Using this approach, we successfully characterized influenza viral morphology, glycoprotein density, and conduct subtomogram averaging of HA glycoproteins. Application of this processing pipeline can aid in the structural characterization of not only influenza viruses, but other pleomorphic viruses and infected cells.