Free Open Source Software Research Articles

Application of automated electron microscopy imaging and machine learning to characterise and quantify nanoparticle dispersion in aqueous media.

SummaryFor many nanoparticle applications it is important to understand dispersion in liquids. For nanomedicinal and nanotoxicological research this is complicated by the often complex nature of the biological dispersant and ultimately this leads to severe limitations in the analysis of the nanoparticle dispersion by light scattering techniques. Here we present an alternative analysis and associated workflow which utilises electron microscopy. The need to collect large, statistically relevant datasets by imaging vacuum dried, plunge frozen aliquots of suspension was accomplished by developing an automated STEM imaging protocol implemented in an SEM fitted with a transmission detector. Automated analysis of images of agglomerates was achieved by machine learning using two free open‐source software tools: CellProfiler and ilastik. The specific results and overall workflow described enable accurate nanoparticle agglomerate analysis of particles suspended in aqueous media containing other potential confounding components such as salts, vitamins and proteins.Lay DescriptionIn order to further advance studies in both nanomedicine and nanotoxicology, we need to continue to understand the dispersion of nanoparticles in biological fluids. These biological environments often contain a number of components such as salts, vitamins and proteins which can lead to difficulties when using traditional techniques to monitor dispersion. Here we present an alternative analysis which utilises electron microscopy. In order to use this approach statistically relevant large image datasets were collected from appropriately prepared samples of nanoparticle suspensions by implementing an automated imaging protocol. Automated analysis of these images was achieved through machine learning using two readily accessible freeware; CellProfiler and ilastik. The workflow presented enables accurate nanoparticle dispersion analysis of particles suspended in more complex biological media.

Three-dimensional (3d) Printing Technology for Aligning Fenestrations in Surgeon Modified Endografts

Introduction: Custom built fenestrated endografts are the preferred option for treating complex paravisceral abdominal aortic aneurysms (AAA). However, when resources and time are unavailable surgeon modified endografts (SMEG) have been reported to be a safe and effective solution. Creation of fenestrations is approximated based on measurements of the physician using imaging software. We sought to determine the applicability of 3D printing a patients' aortic segment in achieving perfect matching of fenestrations with target vessels in SMEGs and to detect factors affecting time needed to achieve this for urgent. Methods: The same vascular surgeon/operator used free open-source software (3DSlicer, MeshMixer) and contrast enhanced computed tomography (CT) series to manually segment the celiac to renal arteries part of the aorta and the first 3 mm of each branch. This volume was then transformed into a hollow 1:1 sized model to be printed with a fused deposition modelling printer (Prusa MK3S). Dedicated 3D-printer software was used to calculate estimated print time with sterilizable co-polyester filament (nGen Flex, ColorFabb). The time for each step of the procedure was recorded along with the 3D model dimensions/volume and filament volume used, CT characteristics and patient details. Continuous variables are expressed as mean +/- SD. Kendall's tau multiple correlations and multiple linear regression were employed to seek relationships between variables and detect independent predictors of time taken. Results: Thirty-one consecutive AAA patients' preoperative CTs were analyzed (7 juxtarenal, 24 infrarenal, 29 men). Each patient's hollow 3D aortic model segmentation needed 13.5+/-4.3 minutes while preparation for 3D printing took 1.3+/-0.9 minutes. Print time was calculated to be 131.3+/-35.2 minutes. Segmentation time displayed a negative correlation with the number of CTs previously segmented by the operator (b = - 0.484, p< 0.001). Print time showed a positive correlation with filament volume (b = 0.6, p< 0.001) and 3D model volume (b = 0.406, p=0.001). 3D model volume was also found to have a positive association with CT interslice distance (CTID) (b=0.628, p< 0.001) and a negative relationship to female sex (b=-0.329, p=0.03). Multiple regression analysis indicated that segmentation time was independently predicted (R squared =0.849, p< 0.001) by CTID, maximum Hounsfield value of the segmentation, number of CTs previously segmented by the operator and the height and sex of the patient. In turn, print time was independently predicted (R squared =0.945, p< 0.001) by filament volume, model dimensions, CTID and the height and sex of the patient. Conclusion: Free open-source software and 3D printers can be used to perfectly align fenestrations on surgeon modified endografts by deploying the endograft within the sterilized 3D printed aortic segment of each patient in an ideally short time frame for urgent cases. Besides aortic volume printed, operator experience and small CT interslice distance can independently reduce time needed.Figure 2Visceral Aortic segment model - top view.View Large Image Figure ViewerDownload Hi-res image Download (PPT) Disclosure: Consulting / Proctoring regional Endologix distributor

Evaluation of the Performance of Online GPS/GNSS Data Processing Services for Monitoring the Land Deformations and Movements

In recent years, the Global Navigation Satellite Services (GNSS) technology has been frequently employed for monitoring the Earth crust deformation and movement. Such applications necessitate high positional accuracy that can be achieved through processing GPS/GNSS data with scientific software such as BERENSE, GAMIT, and GIPSY-OSIS. Nevertheless, these scientific softwares are sophisticated and have not been published as free open source software. Therefore, this study has been conducted to evaluate an alternative solution, GNSS online processing services, which may obtain this privilege freely. In this study, eight years of GNSS raw data for TEHN station, which located in Iran, have been downloaded from UNAVCO website on a daily basis. Furthermore, TEHN GNSS observations are processed with CSRS-PPP, which is based on Precise Point Positioning (PPP) algorithm, and OPUS, which is based on double difference (DD) algorithm, to compare between these two techniques in terms of station velocity estimation and Earth deformation. On the other hand, TEHN station solutions that produce via scientific software, GIPSY-OSIS, are obtained from Nevada Geodetic Laboratory (NGL) website for data validation. Eventually, the results show that both GNSS online processing services (CSRS-PPP and OPUS) are credibly efficient to estimate station velocities, while CSRS-PPP trustworthy service for monitoring the Earth deformation. &#x0D;

EP.46MuscleViz: free open-source software for muscle weakness visualization

EP.46MuscleViz: free open-source software for muscle weakness visualization

SPH Modeling of Water-Related Natural Hazards

This paper collects some recent smoothed particle hydrodynamic (SPH) applications in the field of natural hazards connected to rapidly varied flows of both water and dense granular mixtures including sediment erosion and bed load transport. The paper gathers together and outlines the basic aspects of some relevant works dealing with flooding on complex topography, sediment scouring, fast landslide dynamics, and induced surge wave. Additionally, the preliminary results of a new study regarding the post-failure dynamics of rainfall-induced shallow landslide are presented. The paper also shows the latest advances in the use of high performance computing (HPC) techniques to accelerate computational fluid dynamic (CFD) codes through the efficient use of current computational resources. This aspect is extremely important when simulating complex three-dimensional problems that require a high computational cost and are generally involved in the modeling of water-related natural hazards of practical interest. The paper provides an overview of some widespread SPH free open source software (FOSS) codes applied to multiphase problems of theoretical and practical interest in the field of hydraulic engineering. The paper aims to provide insight into the SPH modeling of some relevant physical aspects involved in water-related natural hazards (e.g., sediment erosion and non-Newtonian rheology). The future perspectives of SPH in this application field are finally pointed out.

Experimental Validation of Spectrum Sensing on Various Transceivers Using Software Defined Radio

Cognitive radio (CR) and software-defined radio (SDR) system technologies provide added flexibility and offer improved spectrum efficiency. Cognitive radio is an obstreperous radio communication and networking technology. It is presently undergoing drastic development due to its potential to resolve many of the problems affecting existing systems. Spectrum sensing is the crucial in empowering technology of CR to sense the existence of primary users or licensed user signals and exploit the spectrum holes. Hence, this paper addresses the design of Energy detection spectrum sensing technique for 16-QAM and 64-QAM transceivers employing SDR testbed. In addition, this paper also addresses the practical signal detection and the impact of various filtering windowing methods on detected signals. Furthermore, the impact of different simulation channels such as dynamic channel model and frequency selective faded channel models with Rayleigh and Rician fadings, are presented by testing the spectrum sensing technique on differential phase shift keying transceiver. For practical proof of the concepts, experimental tests are performed using SDR testbed that employs universal software radio peripheral N210 as hardware platform and GNU Radio as an open source free software platform. Therefore, I have reduced the cost of implementation drastically.

Detection of regime shifts in the environment: testing “STARS” using synthetic and observed time series

Abstract While marine populations change all the time, sometimes regime shifts involve an entire ecosystem, resulting in crucial and sometimes permanent alterations in the ecosystem trophic web and services. A commonly used method to detect shifts in marine systems is the Sequential t-test Analysis of Regime Shifts (STARS). In this work, we chose to analyse the limits and performance of STARS because of its free open-source software and wide use. For the first time, we tested the STARS algorithm using synthetic time series and autoregressive integrated moving average time series, designed to resemble natural observations. We then applied the information obtained from these tests to investigate the STARS detections on an observed time series, that of Calanus finmarchicus in the North Sea. Our tests indicated that in no experiments did STARS detect 100% of the artificial change points at the exact time of the shift. In most cases, STARS tended to anticipate the shift by a few time units. Overall, we determined STARS to be a good method to detect shifts in observed natural time series, so long as the exact time of the shift is not necessary and the possibility of false positives is taken into account.

Dasymetric Mapping Using UAV High Resolution 3D Data within Urban Areas

Multi-temporal analysis of census small-area microdata is hampered by the fact that census tract shapes do not often coincide between census exercises. Dasymetric mapping techniques provide a workaround that is nonetheless highly dependent on the quality of ancillary data. The objectives of this work are to: (1) Compare the use of three spatial techniques for the estimation of population according to census tracts: Areal interpolation and dasymetric mapping using control data—building block area (2D) and volume (3D); (2) demonstrate the potential of unmanned aerial vehicle (UAV) technology for the acquisition of control data; (3) perform a sensitivity analysis using Monte Carlo simulations showing the effect of changes in building block volume (3D information) in population estimates. The control data were extracted by a (semi)-automatic solution—3DEBP (3D extraction building parameters) developed using free open source software (FOSS) tools. The results highlight the relevance of 3D for the dasymetric mapping exercise, especially if the variations in height between building blocks are significant. Using low-cost UAV backed systems with a FOSS-only computing framework also proved to be a competent solution with a large scope of potential applications.

New, simple and reliable volumetric calculation technique in incisional hernias with loss of domain.

The management of hernias with loss of domain is a challenging problem. It has been shown that the volume of the incisional hernia/peritoneal volume ratio <20% was a predictive factor for tension-free fascia closure, after pre-operative pneumoperitoneum preparation (Goni Moreno technique). In this study, we propose an easy, reliable and fast technique to perform volumetric calculation, by the surgeon alone. 3D slicer software (free open-source software) was used to calculate with precision the intra-peritoneal and intra-hernia volumes, and to create a 3D reconstruction of both volumes. The measurement technique is described step by step using detailed figures and videos. The method was used to calculate the volumes for five consecutive patients, managed between January 2018 and March 2019. All the five patients had a ratio greater than 20% and, therefore, received a PPP program. The effectiveness of the procedure is objectified by the increase of the intraabdominal volume and the reduction of the incisional hernia/peritoneal volume ratio. The feasibility of a tension-free fascia closure was confirmed for the five patients. In addition to a standardized definition of "loss of domain", a standardized volumetric technique, easy to reproduce, needs to be adopted. Our method can be done by any surgeon with basic computer skills and radiological knowledge in an autonomous and a fast manner, thus helping to select the right technique for the right patient.

Remote Sensing in Forest Management

Abstract Forest management, as a component of the management of natural protected areas, has the mission to adopt the most effective measures in relation to climate change. The forest management activity is based on management plans drawn up for a period of 10 years, a period appreciated, until recently, to be sufficient for management plans to be considered up to date. Their updating is done with the data provided in field by the rangers through direct observations and measurements, but the accuracy of these data is complemented by data obtained through modern technologies. Analyses of the distribution of forest vegetation, its composition and its evolution, both in time and in the area, and last but not least, the technical measures for implementing the most effective treatments for preserving its health, the optimal structure and biomass production is made using the latest technology, such as Free Open Source Software and GIS. Recent services provided free of charge by some remote sensing operators make it possible to adopt the most appropriate technical measures, real-time tracking of their implementation and expected results. This paper aims to bring to light some of the most useful free remote sensing services and how to use them.

Ground Deformation Identification related to 2018 Lombok Earthquake Series based on Sentinel-1 Data

Lombok Island was hit by a series of earthquakes in July and August 2018 with magnitude 6 class. This series of earthquakes resulted in fatalities and material losses that even reached Sumbawa Island to the east of Lombok Island. The earthquake was triggered by Flores back arc thrust resulting in ground deformation. Ground deformation can be identified by satellite-based remote sensing method. The Sentinel-1A and Sentinel-1B satellites are two satellites carrying C-band SAR sensors with a temporal resolution of 12 days each for the same orbit, and the difference in time between the two is 6 days. Therefore, ground deformation related to seismo-tectonic or volcanic activities can be identified by interfering two SAR images (interferometric synthetic aperture radar or InSAR) at least in 6 days. By utilizing Sentinel Application Platform (SNAP) a free open source software (FOSS) and combining with other InSAR software, an interferogram that represents line of sight displacement (LOS) between ground and satellite can be generated. Line of sight displacement can then be interpreted as ground deformation signals. It is shown that the series of Lombok earthquake cause an uplift up to 70cm and subsidence up to 25cm. This deformation affects areas around epicentre. A field survey was conducted to obtain information directly and it was seen that the ground deformation that was identified with the InSAR technique were consistent with the findings in the field. This shows the advantages of remote sensing in terms of ability to cover a wide area in a short time.

Collect Earth: An online tool for systematic reference data collection in land cover and use applications

Land cover monitoring efforts are important for resource planning and ecosystem services in many countries. Collect Earth Online (CEO) is a new, free open source and user-friendly software tool for land monitoring. It is the product of a collaborative effort between NASA, Food and Agriculture Organization of the United Nations (FAO), US Forest Service and Google. This paper provides a full overview of CEO's structure and functionality. Based on the cloud, CEO's structure supports simultaneous data entry by multiple users. No desktop installation is required and only an internet connection is required setting minimal requirements for using the software. Google Earth Engine widgets can be created for assisted plot interpretation such as image collection, time series graphs featuring indices such as Normalized Difference Vegetation Index (NDVI) and related statistics. We also provide a case study and related findings from a CEO workshop held in Myanmar.

Analyzing and Managing Complex Software Ecosystems: A Framework to Understand Value in Information Systems

Managing complex software ecosystems, such as free open source software projects, is crucial for software-producing organizations. We present a framework that helps visualize complex ecosystem settings, gain insights on value engines, and describe relationships between the ecosystem partners.

Determining efficient values for the thermophysical properties of bulk materials

A procedure has been devised for determining the effective thermophysical properties of bulk materials with different granulometric and material composition, based on the integration of discrete and continuous models of media. The problem on the mechanical-thermal state of a cylindrical layer of bulk material has been stated in order to determine its effective thermophysical properties. Based on the discrete-continuous perceptions of bulk media, an approach has been suggested and a procedure has been devised for solving the problem set. The algorithm for determining effective values of thermophysical properties of bulk materials has been constructed. Numerical implementation of the developed procedure was performed using free open source software (LIGGGHTS, ParaView). The proposed procedure makes it possible to determine effective values for the thermophysical properties of a bulk material (bulk density, effective thermal conductivity coefficient and the effective value for isobaric mass heat capacity) with arbitrary material and granulometric composition. In this case, there is a need for a minimum volume of complex and costly experimental studies with subsequent numerical simulation of the process of the mechanical-thermal state of the examined bulk material. In this case, the true physical properties can be acquired from reference books. Using an example of model material, its effective thermophysical properties have been defined for different granulometric composition and the verification of the developed procedure has been performed. It was established that data on the effective thermal conductivity calculation based on the devised procedure differ from data obtained based on the theoretical averaged dependences, within 0.8‒9.0 %. The reported results are useful for numerical analysis in the continual approximation of thermal modes of the processes and equipment where bulk materials are used

Introduction to This Special Issue on Open Design at the Intersection of Making and Manufacturing

ABSTRACT What is ‘open design’ and who gets to say what it is? In the emerging body of literature on open design, there is a clear alignment to the values and practices of free culture and open source software and hardware. Yet this same literature includes multiple, sometimes even contradictory strands of technology practice and research. These different perspectives can be traced back to free culture advocates from the 1970s to the 1990s who formulated the ideal of the internet as inherently empowering, democratizing, and countercultural. However, more recent approaches include feminist and critical interventions into hacking and making as well as corporate strategies of “open innovation” that bring end-users and consumers into the design process. What remains today seems to fall into two schools of thought. On one hand, we have the celebratory endorsements of ‘openness’ as applied to technology and design. On the other hand, we have a continuous and expanding critique of these very ideals and questions, where that critique identifies persisting forms of racial, gender, age, and class-based exclusions, and questions about the relationship between open design, labor and power remain largely unanswered.

FeatureSelect: a software for feature selection based on machine learning approaches

BackgroundFeature selection, as a preprocessing stage, is a challenging problem in various sciences such as biology, engineering, computer science, and other fields. For this purpose, some studies have introduced tools and softwares such as WEKA. Meanwhile, these tools or softwares are based on filter methods which have lower performance relative to wrapper methods. In this paper, we address this limitation and introduce a software application called FeatureSelect. In addition to filter methods, FeatureSelect consists of optimisation algorithms and three types of learners. It provides a user-friendly and straightforward method of feature selection for use in any kind of research, and can easily be applied to any type of balanced and unbalanced data based on several score functions like accuracy, sensitivity, specificity, etc.ResultsIn addition to our previously introduced optimisation algorithm (WCC), a total of 10 efficient, well-known and recently developed algorithms have been implemented in FeatureSelect. We applied our software to a range of different datasets and evaluated the performance of its algorithms. Acquired results show that the performances of algorithms are varying on different datasets, but WCC, LCA, FOA, and LA are suitable than others in the overall state. The results also show that wrapper methods are better than filter methods.ConclusionsFeatureSelect is a feature or gene selection software application which is based on wrapper methods. Furthermore, it includes some popular filter methods and generates various comparison diagrams and statistical measurements. It is available from GitHub (https://github.com/LBBSoft/FeatureSelect) and is free open source software under an MIT license.

Low cost bench scale apparatus for measuring the thermal resistance of multilayered textile fabric against radiative and contact heat transfer

Radiation is the main medium of heat transfer from fire to firefighter. The protective clothing a firefighter wears is required to have good capability to resist this incoming heat radiation. Various fibre, fabric and other materials offer different levels of protection against heat radiation. The instruments used to measure the protective capability of fabric against radiant heat are normally expensive and may unable to measure heat resistance behind each layer of a multilayer combination simultaneously. In the current study, a bench scale and easy-to-operate instrument has been developed to measure the radiative and contact heat protection performance of textile fabric/clothing in multilayered configurations. Normal wooden frames, domestic aluminum foil, free open source software and high precision temperature sensors are used to develop the instrument. This instrument can be a very useful tool to gain primary understanding of the radiative heat protection of any material in single or multilayered configuration.

Imaging and printing in plastic and reconstructive surgery part 1: established techniques

Background: An increasing number of reconstructive surgeons are using modern imaging technologies for preoperative planning and intraoperative surgical guidance. Conventional imaging modalities such as CT and MRI are relatively affordable and widely accessible and offer powerful functionalities. In the first of a two-part series, we evaluate established three-dimensional (3D) imaging and printing techniques based on CT and MRI used in plastic and reconstructive surgery. Method: A review of the published English literature dating from 1950 to 2017 was taken using databases such as PubMed, MEDLINE®, Web of Science and EMBASE. Result: In plastic and reconstructive surgery, the most commonly used, free software platforms are 3D Slicer (Surgical Planning Laboratory, Boston, MA, USA) and OsiriX (Pixmeo, Geneva, Switzerland). Perforator mapping using 3D-reconstructed images from computed tomography angiography (CTA) and magnetic resonance angiography (MRA) is commonly used for preoperative planning. Three- dimensional volumetric analysis using current software techniques remains labour-intensive and reliant on operator experience. Three-dimensional printing has been investigated extensively since its introduction. As more free open-source software suites and affordable 3D printers become available, 3D printing is becoming more accessible for clinicians. Conclusion: Numerous studies have explored the application of 3D-rendered conventional imaging modalities for perforator mapping, volumetric analysis and printing. However, there is a lack of comprehensive review of all established 3D imaging and printing techniques in a language suitable for clinicians.

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization.

Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available at https://github.com/linzhi2013/MitoZ.

MQTT for IoT-based Applications in Smart Cities

This research presents a study on the use of the MQTT communications protocol for the Internet of Things in Smart City applications. A network model is proposed and a typical practical scenario is developed based on MQTT protocol, that cope with the requirements of some Smart City applications, mainly those which use event-based messages. Many market-available embedded electronic systems were employed for this scenario including the inexpensive Wi-Fi platform ESP8266, Arduino, Raspberry, in addition to some sensors and actuators. The network model is chosen based on the TCP/IP model, and the application layer is totally depending on the MQTT protocol that employs JavaScript Object Notation (JSON) to solve the problem of interoperability. To evaluate the protocol for small-to-medium, IoT-based, business applications of Smart Cities, some available free Open Source Software (OSS) of MQTT servers and clients were compared and tested against latency over the cloud. The protocol shows good results for cloud-based, small-to-medium business applications that depend on event-based message-oriented communication paradigms. Since the protocol defines three levels of quality of service (QoS), the simulations and the tests were conducted for QoS type zero (QoS0) to get the best results.