scholarly journals A Do-It-Yourself Hyperspectral Imager Brought to Practice with Open-Source Python

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1072
Author(s):  
Kimmo Aukusti Riihiaho ◽  
Matti Aleksanteri Eskelinen ◽  
Ilkka Pölönen
Keyword(s):  
Open Source ◽  
Hyperspectral Imaging ◽  
3D Models ◽  
Research Groups ◽  
Financial Status ◽  
Software Artifact ◽  
Correction Problem ◽  
Do It Yourself

Commercial hyperspectral imagers (HSIs) are expensive and thus unobtainable for large audiences or research groups with low funding. In this study, we used an existing do-it-yourself push-broom HSI design for which we provide software to correct for spectral smile aberration without using an optical laboratory. The software also corrects an aberration which we call tilt. The tilt is specific for the particular imager design used, but correcting it may be beneficial for other similar devices. The tilt and spectral smile were reduced to zero in terms of used metrics. The software artifact is available as an open-source Github repository. We also present improved casing for the imager design, and, for those readers interested in building their own HSI, we provide print-ready and modifiable versions of the 3D-models required in manufacturing the imager. To our best knowledge, solving the spectral smile correction problem without an optical laboratory has not been previously reported. This study re-solved the problem with simpler and cheaper tools than those commonly utilized. We hope that this study will promote easier access to hyperspectral imaging for all audiences regardless of their financial status and availability of an optical laboratory.

Open-source and do-it-yourself microfluidics

2021 ◽  
pp. 130624
Author(s):  
Joong Ho Shin ◽  
Sungyoung Choi
Keyword(s):  
Open Source ◽  
Do It Yourself

scholarly journals Do-it-yourself networks: a novel method of generating weighted networks

2017 ◽  
Vol 4 (11) ◽  
pp. 171227 ◽  
Author(s):  
D. W. Shanafelt ◽  
K. R. Salau ◽  
J. A. Baggio
Keyword(s):  
Social Sciences ◽  
Open Source ◽  
Network Theory ◽  
Source Code ◽  
Ecological Systems ◽  
Species Dispersal ◽  
Social Ecological Systems ◽  
Social Ecological ◽  
Novel Method ◽  
Do It Yourself

Network theory is finding applications in the life and social sciences for ecology, epidemiology, finance and social–ecological systems. While there are methods to generate specific types of networks, the broad literature is focused on generating unweighted networks. In this paper, we present a framework for generating weighted networks that satisfy user-defined criteria. Each criterion hierarchically defines a feature of the network and, in doing so, complements existing algorithms in the literature. We use a general example of ecological species dispersal to illustrate the method and provide open-source code for academic purposes.

scholarly journals Microvessel Chaste: An Open Library for Spatial Modelling of Vascularized Tissues

2017 ◽  
Author(s):  
J.A. Grogan ◽  
A.J. Connor ◽  
B. Markelc ◽  
R.J. Muschel ◽  
P.K. Maini ◽  
...  
Keyword(s):  
Open Source ◽  
Tumour Growth ◽  
Spatial Models ◽  
3D Models ◽  
Tissue Growth ◽  
Coronary Perfusion ◽  
Analysis Model ◽  
User Friendly

AbstractSpatial models of vascularized tissues are widely used in computational physiology, to study for example, tumour growth, angiogenesis, osteogenesis, coronary perfusion and oxygen delivery. Composition of such models is time-consuming, with many researchers writing custom software for this purpose. Recent advances in imaging have produced detailed three-dimensional (3D) datasets of vascularized tissues at the scale of individual cells. To fully exploit such data there is an increasing need for software that allows user-friendly composition of efficient, 3D models of vascularized tissue growth, and comparison of predictions with in vivo or in vitro experiments and other models. Microvessel Chaste is a new open-source library for building spatial models of vascularized tissue growth. It can be used to simulate vessel growth and adaptation in response to mechanical and chemical stimuli, intra- and extra-vascular transport of nutrient, growth factor and drugs, and cell proliferation in complex 3D geometries. The library provides a comprehensive Python interface to solvers implemented in C++, allowing user-friendly model composition, and integration with experimental data. Such integration is facilitated by interoperability with a growing collection of scientific Python software for image processing, statistical analysis, model annotation and visualization. The library is available under an open-source Berkeley Software Distribution (BSD) licence at https://jmsgrogan.github.io/MicrovesselChaste. This article links to two reproducible example problems, showing how the library can be used to model tumour growth and angiogenesis with realistic vessel networks.

scholarly journals BIM Open Source Software (OSS) for the documentation of cultural heritage

2016 ◽  
Vol 7 (15) ◽  
pp. 28 ◽  
Author(s):  
Sotiris Logothetis ◽  
Efstratios Stylianidis
Keyword(s):  
Cultural Heritage ◽  
Open Source ◽  
Software Industry ◽  
3D Models ◽  
Design Data ◽  
Industry Foundation Classes ◽  
Digital Reconstruction ◽  
Building Information ◽  
Recent Developments ◽  
Digital Documentation

<p class="VARAbstract">The Building Information Modelling (BIM) software enables the users to communicate and design, understand appearance, performance and cost in the spatial and urban design process. Another important use of the BIM technology is the documentation and 3D reconstruction of cultural heritage monuments. The appropriate BIM software equips the users with tools to easily capture and analyse concepts and maintain the coordination of design data through documentation and 3D modelling. Many developments come up in the BIM field and software industry for design, construction-reconstruction, restoration and management of the cultural heritage 3D models, using BIM tools; mainly commercial as well as free or open source. Nevertheless, recently the growing popularity of open source has altered the landscape in software industry, as they attract many users.</p><p class="VARAbstract">This paper presents a review of some recent research on the topic. We review the recent developments focusing on the OSS that can be used at various stages of BIM process in the digital documentation of cultural heritage. The results show that there is more preference in the commercial software due to the fact that the OSS is not yet complete and covers all stages of the BIM process. However, lately we have the Edificius in architectural BIM design and “BIM Vision” as Industry Foundation Classes (IFC) model viewer that try to attract as many users as possible. These tools are free and they could well be used for the digital reconstruction of cultural heritage.</p>

“Going Rogue”

2018 ◽  
Vol 4 (2) ◽  
pp. 137-156
Author(s):  
Samantha D. Gottlieb ◽  
Jonathan Cluck
Keyword(s):  
Open Source ◽  
Treatment Guidelines ◽  
Artificial Pancreas ◽  
Medical Model ◽  
Glucose Monitoring ◽  
Diabetes Research ◽  
Medical Surveillance ◽  
Patient Centered ◽  
Do It Yourself ◽  
Medical Category

Abstract This paper explores our collaborative STS and anthropological project with type 1 diabetes (T1D) hardware “hacking” communities, whose work focuses on reverse-engineering and extracting data from medical devices such as insulin pumps and continuous glucose monitoring systems (CGMS) to create do-it-yourself artificial pancreas systems (APS). Rather than using these devices within their prescriptive and prescribed purposes (surveillance and treatment monitoring), these “hackers” repurpose, reinterpret, and redirect of the possibilities of medical surveillance data in order to reshape their own treatment. Through “deliberate non-compliance” (Scibilia 2017) with cliniciandeveloped treatment guidelines, T1D device hackers deliberatively engage with clinicians’ conceptions and formulations of what constitutes “good treatment” and empower themselves in discussions about the effectiveness of treatment guidelines. Their non-compliance is, however, neither negligence, as implied by the medical category of patients who fail to comply with clinical orders, nor ignorance, but a productive and creative response to their embodied expertise, living with a chronic and potentially deadly condition. Our interlocutors’ explicit connections with the free and open source software principles suggests the formation of a “recursive public” (Kelty 2008) in diabetes research and care practices, from a patient-centered “medical model” to a diverse and divergent patient-led model. The philosophical and ethical underpinnings of the open source and collaborative strategies these patients draw upon radically reshape the principles that drive the commercial health industry and government regulatory structures.

scholarly journals A workflow to generate physical 3D models of cerebral aneurysms applying open source freeware for CAD modeling and 3D printing

2019 ◽  
Vol 17 ◽  
pp. 1-6 ◽  
Author(s):  
Alba Scerrati ◽  
Federica Trovalusci ◽  
Alessio Albanese ◽  
Gennaro Salvatore Ponticelli ◽  
Vincenzo Tagliaferri ◽  
...  
Keyword(s):  
3D Printing ◽  
Open Source ◽  
Cerebral Aneurysms ◽  
3D Models ◽  
Cad Modeling

scholarly journals Practical Aspects of Multiwavelength Analytical Ultracentrifugation

Instruments ◽  
2019 ◽  
Vol 3 (1) ◽  
pp. 23 ◽  
Author(s):  
Joseph Pearson ◽  
Helmut Cölfen
Keyword(s):  
Open Source ◽  
Broad Spectrum ◽  
Analytical Ultracentrifugation ◽  
Experimental Results ◽  
Research Groups ◽  
High Quality ◽  
Detection Systems ◽  
Operational Information ◽  
Optical Alignment ◽  
Scientific Fields

Open-source Multiwavelength Analytical Ultracentrifugation (MWL-AUC) detection systems have been evolving for over a decade. Continual advances emerging out of several research groups have brought the instrumentation technology to increasingly higher levels of performance. The capabilities of MWL-AUC have been documented in many publications, demonstrating the applicability of broad spectrum absorbance acquisitions in analytical ultracentrifugation to a wide array of scientific fields. Despite numerous examples of the usefulness and unique advantages of MWL-AUC, the adoption of the technology by more research groups has been slow. The complexity of the hardware, integration within an ultracentrifuge platform and lack of practical construction and operational information is the likely source of reluctance. Here, we clearly describe the challenges facing a researcher considering adopting MWL-AUC technology in their own laboratories, and provide the information necessary to implement and operate a MWL-AUC system. The discussion includes details of detector assembly, optical alignment, and acquisition parameter settings necessary to achieve high quality experimental results.

scholarly journals Open source approaches to establishingRoseobacterclade bacteria as synthetic biology chassis for biogeoengineering

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2031 ◽  
Author(s):  
Yanika Borg ◽  
Aurelija Marija Grigonyte ◽  
Philipp Boeing ◽  
Bethan Wolfenden ◽  
Patrick Smith ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Open Source ◽  
Collaborative Group ◽  
Positive Contribution ◽  
Bacterial Cells ◽  
Dna Manipulation ◽  
Bioinformatic Tools ◽  
Dinoroseobacter Shibae ◽  
Do It Yourself ◽  
Plankton Communities

Aim.The nascent field of bio-geoengineering stands to benefit from synthetic biologists’ efforts to standardise, and in so doing democratise, biomolecular research methods.Roseobacterclade bacteria comprise 15–20% of oceanic bacterio-plankton communities, making them a prime candidate for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic. Developments such as the increasing affordability of DNA synthesis and laboratory automation continue to foster the establishment of a global ‘do-it-yourself’ research community alongside the more traditional arenas of academe and industry. As a collaborative group of citizen, student and professional scientists we sought to test the following hypotheses: (i) that an incubator capable of cultivating bacterial cells can be constructed entirely from non-laboratory items, (ii) that marine bacteria from theRoseobacterclade can be established as a genetically tractable synthetic biology chassis using plasmids conforming to the BioBrickTMstandard and finally, (iii) that identifying and subcloning genes from aRoseobacterclade species can readily by achieved by citizen scientists using open source cloning and bioinformatic tools.Method.We cultivated threeRoseobacterspecies,Roseobacter denitrificans,Oceanobulbus indolifexandDinoroseobacter shibae. For each species we measured chloramphenicol sensitivity, viability over 11 weeks of glycerol-based cryopreservation and tested the effectiveness of a series of electroporation and heat shock protocols for transformation using a variety of plasmid types. We also attempted construction of an incubator-shaker device using only publicly available components. Finally, a subgroup comprising citizen scientists designed and attempted a procedure for isolating the cold resistanceanf1gene fromOceanobulbus indolifexcells and subcloning it into a BioBrickTMformatted plasmid.Results.All species were stable over 11 weeks of glycerol cryopreservation, sensitive to 17 µg/mL chloramphenicol and resistant to transformation using the conditions and plasmids tested. An incubator-shaker device, ‘UCLHack-12’ was assembled and used to cultivate sufficient quantity ofOceanobulbus indolifexcells to enable isolation of theanf1gene and its subcloning into a plasmid to generate the BioBrickTMBBa_K729016.Conclusion.The process of ‘de-skilling’ biomolecular techniques, particularly for relatively under-investigated organisms, is still on-going. However, our successful cell growth and DNA manipulation experiments serve to indicate the types of capabilities that are now available to citizen scientists. Science democratised in this way can make a positive contribution to the debate around the use of bio-geoengineering to address oceanic pollution or climate change.

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.

Sign in / Sign up

Export Citation Format

Share Document