scholarly journals scAnt—an open-source platform for the creation of 3D models of arthropods (and other small objects)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11155
Author(s):  
Fabian Plum ◽  
David Labonte
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Synthetic Data ◽  
3D Models ◽  
Depth Of Field ◽  
Multiple Perspectives ◽  
Automated Generation ◽  
Volume Measurements ◽  
The Creation ◽  
Area And Volume

We present scAnt, an open-source platform for the creation of digital 3D models of arthropods and small objects. scAnt consists of a scanner and a Graphical User Interface, and enables the automated generation of Extended Depth Of Field images from multiple perspectives. These images are then masked with a novel automatic routine which combines random forest-based edge-detection, adaptive thresholding and connected component labelling. The masked images can then be processed further with a photogrammetry software package of choice, including open-source options such as Meshroom, to create high-quality, textured 3D models. We demonstrate how these 3D models can be rigged to enable realistic digital specimen posing, and introduce a novel simple yet effective method to include semi-realistic representations of approximately planar and transparent structures such as wings. As a result of the exclusive reliance on generic hardware components, rapid prototyping and open-source software, scAnt costs only a fraction of available comparable systems. The resulting accessibility of scAnt will (i) drive the development of novel and powerful methods for machine learning-driven behavioural studies, leveraging synthetic data; (ii) increase accuracy in comparative morphometric studies as well as extend the available parameter space with area and volume measurements; (iii) inspire novel forms of outreach; and (iv) aid in the digitisation efforts currently underway in several major natural history collections.

Open-source software for the application of microphone array methods

2017 ◽  
Vol 48 (3-4) ◽  
pp. 44-51 ◽  
Author(s):  
Gert Herold ◽  
Ennes Sarradj
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Time Domain ◽  
Microphone Array ◽  
Synthetic Data ◽  
Object Oriented ◽  
Source Characterization ◽  
Acoustic Source ◽  
Array Data ◽  
Flexible Programming

The open-source Python library Acoular is aimed at the processing of microphone array data. It features a number of algorithms for acoustic source characterization in time domain and frequency domain. The modular, object-oriented architecture allows for flexible programming and a multitude of applications. This includes the processing of measured array data, the mapping of sources, the filtering of subcomponent noise, and the generation of synthetic data for test purposes. Several examples illustrating its versatility are given, as well as one example for implementing a new algorithm into the package.

scholarly journals OPEN SOURCE CLOUD-BASED TECHNOLOGIES FOR BIM

2018 ◽  
Vol XLII-2 ◽  
pp. 607-614 ◽  
Author(s):  
S. Logothetis ◽  
E. Karachaliou ◽  
E. Valari ◽  
E. Stylianidis
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Research Work ◽  
3D Models ◽  
Web Interface ◽  
Multiple Stakeholders ◽  
Architectural Engineering ◽  
Starting Point ◽  
Cloud Technologies ◽  
Survey Approach

This paper presents a Cloud-based open source system for storing and processing data from a 3D survey approach. More specifically, we provide an online service for viewing, storing and analysing BIM. Cloud technologies were used to develop a web interface as a BIM data centre, which can handle large BIM data using a server. The server can be accessed by many users through various electronic devices anytime and anywhere so they can view online 3D models using browsers. Nowadays, the Cloud computing is engaged progressively in facilitating BIM-based collaboration between the multiple stakeholders and disciplinary groups for complicated Architectural, Engineering and Construction (AEC) projects. Besides, the development of Open Source Software (OSS) has been rapidly growing and their use tends to be united. Although BIM and Cloud technologies are extensively known and used, there is a lack of integrated open source Cloud-based platforms able to support all stages of BIM processes. The present research aims to create an open source Cloud-based BIM system that is able to handle geospatial data. In this effort, only open source tools will be used; from the starting point of creating the 3D model with FreeCAD to its online presentation through BIMserver. Python plug-ins will be developed to link the two software which will be distributed and freely available to a large community of professional for their use. The research work will be completed by benchmarking four Cloud-based BIM systems: Autodesk BIM 360, BIMserver, Graphisoft BIMcloud and Onuma System, which present remarkable results.

scholarly journals Phenomenal: An automatic open source library for 3D shoot architecture reconstruction and analysis for image-based plant phenotyping

2019 ◽  
Author(s):  
Simon Artzet ◽  
Tsu-Wei Chen ◽  
Jérôme Chopard ◽  
Nicolas Brichet ◽  
Michael Mielewczik ◽  
...  
Keyword(s):  
Open Source ◽  
High Throughput ◽  
Synthetic Data ◽  
3D Models ◽  
Plant Phenotyping ◽  
Published Data ◽  
Data Sets ◽  
Quantitative Measurements ◽  
Workflow System ◽  
Architectural Features

AbstractIn the era of high-throughput visual plant phenotyping, it is crucial to design fully automated and flexible workflows able to derive quantitative traits from plant images. Over the last years, several software supports the extraction of architectural features of shoot systems. Yet currently no end-to-end systems are able to extract both 3D shoot topology and geometry of plants automatically from images on large datasets and a large range of species. In particular, these software essentially deal with dicotyledons, whose architecture is comparatively easier to analyze than monocotyledons. To tackle these challenges, we designed the Phenomenal software featured with: (i) a completely automatic workflow system including data import, reconstruction of 3D plant architecture for a range of species and quantitative measurements on the reconstructed plants; (ii) an open source library for the development and comparison of new algorithms to perform 3D shoot reconstruction and (iii) an integration framework to couple workflow outputs with existing models towards model-assisted phenotyping. Phenomenal analyzes a large variety of data sets and species from images of high-throughput phenotyping platform experiments to published data obtained in different conditions and provided in a different format. Phenomenal has been validated both on manual measurements and synthetic data simulated by 3D models. It has been also tested on other published datasets to reproduce a published semi-automatic reconstruction workflow in an automatic way. Phenomenal is available as an open-source software on a public repository.

scholarly journals Methodology for creating 3D paper unfolded models with complex geometry using open-source software and resources with free personal and commercial license

2018 ◽  
Vol 2 (1) ◽  
pp. 39-46
Author(s):  
Kremena Tsankova Markova ◽  
Tihomir Atanassov Dovramadjiev ◽  
Ginka Velikova Jecheva
Keyword(s):  
Exact Sequence ◽  
Open Source ◽  
Design Process ◽  
Open Source Software ◽  
Complex Geometry ◽  
Three Dimensional ◽  
Functional Capabilities ◽  
The Creation ◽  
Technological Means ◽  
Three Dimensional Models

The creation of 3D paper unfolded models with complex geometry requires precision in the design process. Achieving this is through the use of accessible resources and modern technological means which possess the necessary technical and functional capabilities. The successful realization of the models is through the use of a structured methodology containing design stages that are defined in the exact sequence. The present study aims to create the unfoldings of complex three-dimensional models by covering the stages of providing accessible resurses with a personal and commercial license that are transformed in sequence until the ready-made variants.

scholarly journals The Right Tools for the Job: The Case for Spatial Science Tool-Building

2020 ◽  
Author(s):  
Geoff Boeing
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Data Science ◽  
Network Science ◽  
Science Literature ◽  
Spatial Network ◽  
Multiple Perspectives ◽  
Development Tool ◽  
The Right ◽  
Tool Building

This paper was presented as the 8th annual Transactions in GIS plenary address at the American Association of Geographers annual meeting in Washington, DC. The spatial sciences have recently seen growing calls for more accessible software and tools that better embody geographic science and theory. Urban spatial network science offers one clear opportunity: from multiple perspectives, tools to model and analyze nonplanar urban spatial networks have traditionally been inaccessible, atheoretical, or otherwise limiting. This paper reflects on this state of the field. Then it discusses the motivation, experience, and outcomes of developing OSMnx, a tool intended to help address this. Next it reviews this tool's use in the recent multidisciplinary spatial network science literature to highlight upstream and downstream benefits of open‐source software development. Tool-building is an essential but poorly incentivized component of academic geography and social science more broadly. To conduct better science, we need to build better tools. The paper concludes with paths forward, emphasizing open-source software and reusable computational data science beyond mere reproducibility and replicability.

scholarly journals FROM OSS CAD TO BIM FOR CULTURAL HERITAGE DIGITAL REPRESENTATION

2017 ◽  
Vol XLII-2/W3 ◽  
pp. 439-445 ◽  
Author(s):  
S. Logothetis ◽  
E. Karachaliou ◽  
E. Stylianidis
Keyword(s):  
Cultural Heritage ◽  
Open Source ◽  
Open Source Software ◽  
Computer Aided Design ◽  
3D Models ◽  
Building Information Modelling ◽  
Information Modelling ◽  
Digital Representations ◽  
Building Information ◽  
Aided Design

The paper illustrates the use of open source Computer-aided design (CAD) environments in order to develop Building Information Modelling (BIM) tools able to manage 3D models in the field of cultural heritage. Nowadays, the development of Free and Open Source Software (FOSS) has been rapidly growing and their use tends to be consolidated. Although BIM technology is widely known and used, there is a lack of integrated open source platforms able to support all stages of Historic Building Information Modelling (HBIM) processes. The present research aims to use a FOSS CAD environment in order to develop BIM plug-ins which will be able to import and edit digital representations of cultural heritage models derived by photogrammetric methods.

The Labor Politics of Scratching an Itch

2011 ◽  
pp. 460-467
Author(s):  
Casey O’Donnell
Keyword(s):  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Economic Structure ◽  
Symbiotic Relationship ◽  
Economic Gain ◽  
Labor Politics ◽  
Educational Foundations ◽  
The Creation

This chapter will focus on the economic and temporal/labor demands of creating free/libre and open source software (FLOSS). It begins by analyzing the economic and educational foundations of those countries most actively involved in FLOSS development, and how that affects the overall demographics of the FLOSS movement. Through examining the symbiotic relationship that the community has with commercial or closed software development, the educational and employment prerequisites, and overwhelming gendered makeup of the movement, we will come to see the movement in new ways. This is supplemented by an examination of how this economic structure could conceivably be exploited for increased economic gain at the expense of those individuals actually involved in the creation of the software. Finally, the chapter concludes by looking at possible ways in which FLOSS software could be opened up more broadly to non-technical software users.

scholarly journals GENERATING ACCURATE 3D MODELS OF ARCHITECTURAL HERITAGE STRUCTURES USING LOW-COST CAMERA AND OPEN SOURCE ALGORITHMS

2017 ◽  
Vol XLII-5/W1 ◽  
pp. 99-104
Author(s):  
M. Zacharek ◽  
P. Delis ◽  
M. Kedzierski ◽  
A. Fryskowska
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Web Application ◽  
Low Cost ◽  
Digital Camera ◽  
Point Clouds ◽  
3D Models ◽  
Dense Image ◽  
Dense Point ◽  
Historical Heritage

These studies have been conductedusing non-metric digital camera and dense image matching algorithms, as non-contact methods of creating monuments documentation.In order toprocess the imagery, few open-source software and algorithms of generating adense point cloud from images have been executed. In the research, the OSM Bundler, VisualSFM software, and web application ARC3D were used. Images obtained for each of the investigated objects were processed using those applications, and then dense point clouds and textured 3D models were created. As a result of post-processing, obtained models were filtered and scaled.The research showedthat even using the open-source software it is possible toobtain accurate 3D models of structures (with an accuracy of a few centimeters), but for the purpose of documentation and conservation of cultural and historical heritage, such accuracy can be insufficient.

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