scholarly journals An open Platform for High-resolution Light-based Control of Microscopic Collectives

Author(s):  
Ana Rubio Denniss ◽  
Thomas E. Gorochowski ◽  
Sabine Hauert

Engineering microscopic collectives of cells or microrobots is challenging due to the often-limited capabilities of the individual agents, our inability to reliably program their motion and local interactions, and difficulties visualising their behaviours. Here, we present a low-cost, modular and open-source Dynamic Optical MicroEnvironment (DOME) and demonstrate its ability to augment microagent capabilities and control collective behaviours using light. The DOME offers an accessible means to study complex multicellular phenomena and implement de-novo microswarms with desired functionalities. Corresponding author(s) Email: [email protected] [email protected]

2020 ◽  
Author(s):  
Ana Rubio Denniss ◽  
Thomas E. Gorochowski ◽  
Sabine Hauert

AbstractEngineering microscopic collectives of cells or microrobots is challenging due to the often-limited capabilities of the individual agents, our inability to program their motion and local interactions, and difficulties visualising their behaviours. Here, we present a low-cost, modular and open-source Dynamic Optical MicroEnvironment (DOME) and demonstrate its ability to augment microagent capabilities and control collective behaviours using light. The DOME offers an accessible means to study complex multicellular phenomena and implement de-novo microswarms with desired functionalities.


Sensors ◽  
2021 ◽  
Vol 21 (2) ◽  
pp. 572
Author(s):  
Mads Jochumsen ◽  
Taha Al Muhammadee Janjua ◽  
Juan Carlos Arceo ◽  
Jimmy Lauber ◽  
Emilie Simoneau Buessinger ◽  
...  

Brain-computer interfaces (BCIs) have been proven to be useful for stroke rehabilitation, but there are a number of factors that impede the use of this technology in rehabilitation clinics and in home-use, the major factors including the usability and costs of the BCI system. The aims of this study were to develop a cheap 3D-printed wrist exoskeleton that can be controlled by a cheap open source BCI (OpenViBE), and to determine if training with such a setup could induce neural plasticity. Eleven healthy volunteers imagined wrist extensions, which were detected from single-trial electroencephalography (EEG), and in response to this, the wrist exoskeleton replicated the intended movement. Motor-evoked potentials (MEPs) elicited using transcranial magnetic stimulation were measured before, immediately after, and 30 min after BCI training with the exoskeleton. The BCI system had a true positive rate of 86 ± 12% with 1.20 ± 0.57 false detections per minute. Compared to the measurement before the BCI training, the MEPs increased by 35 ± 60% immediately after and 67 ± 60% 30 min after the BCI training. There was no association between the BCI performance and the induction of plasticity. In conclusion, it is possible to detect imaginary movements using an open-source BCI setup and control a cheap 3D-printed exoskeleton that when combined with the BCI can induce neural plasticity. These findings may promote the availability of BCI technology for rehabilitation clinics and home-use. However, the usability must be improved, and further tests are needed with stroke patients.


2020 ◽  
Vol 10 (2) ◽  
pp. 2258-2271

Inceptions for chemical process automation are presented in this study. A chemical process demonstrated by neutralization reaction was designed, built, and tested experimentally towards evaluating automation and control algorithms through the Arduino Mega platform. The main objective parameter in this work was selected to be the product pH value, which was evaluated based on several scenarios that targeted various changes in direct and indirect effects. Two main branched ideas were investigated in this study; the first was dealt with the application of Arduino board in the automation of chemical process; the second was dedicated to studying integration of Arduino board in controlling the targeted pH parameter in the product side. Upon examining different automation scenarios, an algorithm was developed to approach the product quality of specific pH and temperature efficiently. The automation algorithm was further developed by integrating the process dynamics and control concepts towards speeding up the pH set point's reach. To make this happen, the pump's speed was corrected and tuned based on the feedback signal from the pH sensor. Consequently, the setpoint was reached in shorter periods, attaining considerable savings in time (≈ 35%). Based on the study outcomes, it is believed that Arduino open source is a challenging and promising low-cost platform, proved useful for mimicking control and automation of chemical processes.


Geosciences ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 356 ◽  
Author(s):  
Alexander R. Groos ◽  
Thalia J. Bertschinger ◽  
Céline M. Kummer ◽  
Sabrina Erlwein ◽  
Lukas Munz ◽  
...  

Unmanned Aerial Vehicles (UAV) are a rapidly evolving tool in geosciences and are increasingly deployed for studying the dynamic processes of the earth’s surface. To assess the potential of autonomous low-cost UAVs for the mapping and monitoring of alpine glaciers, we conducted multiple aerial surveys on the Kanderfirn in the Swiss Alps in 2017 and 2018 using open hardware and software of the Paparazzi UAV project. The open-source photogrammetry software OpenDroneMap was tested for the generation of high-resolution orthophotos and digital surface models (DSMs) from aerial imagery and cross-checked with the well-established proprietary software Pix4D. Accurately measured ground control points served for the determination of the geometric accuracy of the orthophotos and DSMs. A horizontal (xy) accuracy of 0.7–1.2 m and a vertical (z) accuracy of 0.7–2.1 m was achieved for OpenDroneMap, compared to a xy-accuracy of 0.3–0.5 m and a z-accuracy of 0.4–0.5 m obtained for Pix4D. Based on the analysis and comparison of different orthophotos and DSMs, surface elevation, roughness and brightness changes from 3 June to 29 September 2018 were quantified. While the brightness of the glacier surface decreased linearly over the ablation season, the surface roughness increased. The mean DSM-based elevation change across the glacier tongue was 8 m, overestimating the measured melting and surface lowering at the installed ablation stakes by about 1.5 m. The presented results highlight that self-built fixed-wing UAVs in tandem with open-source photogrammetry software are an affordable alternative to commercial remote-sensing platforms and proprietary software. The applied low-cost approach also provides great potential for other regions and geoscientific disciplines.


2020 ◽  
Vol 10 (14) ◽  
pp. 4696 ◽  
Author(s):  
Luis I. Minchala ◽  
Jonnathan Peralta ◽  
Paul Mata-Quevedo ◽  
Jaime Rojas

This paper presents a performance evaluation of the development of the instrumentation, communications and control systems of a two-tank process by using low-cost hardware and open source software. The hardware used for automating this process consists of embedded platforms (Arduino and Raspberry Pi) integrated into programmable logic controllers (PLCs), which are connected to a supervisory control and data acquisition (SCADA) system implemented with an open source Industrial Internet of Things (IIoT) platform. The main purpose of the proposed approach is to evaluate low-cost automation solutions (hardware and software) within the framework of modern industry requirements in order to determine whether these technologies could be enabling factors of IIoT. The proposed control strategy for regulating tank levels combines the classic PID algorithm and the fuzzy gain scheduling PID (FGS-PID) approach. Fault detection capabilities are also enabled for the system through a fault detection and diagnosis module (FDD) implemented with an extended Kalman filter (EKF). The distributed controller’s (DC) algorithms are embedded into the PLC’s processors in order to demonstrate the flexibility of the proposed system. Additionally, a remote human to machine interface (HMI) is deployed through a web client of the IIoT application. Experimental results show the proper operation of the overall system.


2017 ◽  
Vol 13 (1) ◽  
Author(s):  
Denisa Kera

RESUMO A cultura maker, definida como um conjunto de experiências que agrupam ferramentas de hardware de código aberto (Weiss 2008; Mellis & Buechley 2011; Ames et al. 2014), de práticas faça-você-mesmo (Ratto & Boler 2014; Ames et al. 2014; Lindtner et al. 2016), promesas da fabricação digital, automática e distribuída (Gershenfeld et al. 2004; Ratto & Ree 2012), e equipamentos para a democratização da ciência (Pearce 2014; Pearce 2012), persiste como um objeto ambiguo de nossas recentes fantasias do design e da política. De um lado, há o surgimento de políticas e interesses governamentais nos EUA, China, Cingapura, Taiwam e Europa, sobre o tal “movimento maker”, levando diretamente ao atual chamado nacionalista do tipo “Faça (o país XYZ) Grande Novamente”. De outro lado, os projetos e atividades maker (experimentações com Arduino, construção de impressoras 3D, montagem de infraestruturas de laboratórios de biologia faça-voçê-mesmo), continuam restritos a um nicho exploratório e privado, mesmo quando são parte de redes informais e transnacionais (Vertesi et al. 2011; Kaiying & Lindtner 2016) que eu denomino “diplomacia geek” (Kera 2015). Sem afirmar claramente qualquer agenda local ou transnacional, os makers faça-você-mesmo negociam de maneira produtiva e criativa várias dicotomias entre o individualismo e o coletivismo, entre os interesses locais e globais, nacionalismo e cosmopolitismo. Eles conectam politica e design através da liminaridade, em experiencias individuais e exploratórias de prototipagem e tinkering, que diferem muito das formas de aquisição de conhecimentos, habilidades e prototipagem típicas dos contextos industriais e acadêmicos. Para explicar a liminaridade na cultura maker, eu expando o trabalho pioneiro de Gabriela Coleman sobre os paradoxos do movimento hacker (e do movimento de software aberto). As redes descentralizadas e transnacionais de makers e hackers são exemplos (tecnológicos) de comunidades e liminaridades (Turner, 1969), que negociam vários objetivos e agendas conflitantes por trás da fabricação, tecnologia e globalização. A cultura maker pode servir a agendas isolacionistas ou cosmopolitas ao mesmo tempo, e ainda abraçar a retórica do código aberto enquanto segue parcialmente patenteada, pirateada e híbrida. Ela mobiliza as esperanças do Sul Global de tecnologias de baixo custo, enquanto performatiza clichés do Vale do Silício e se utiliza do trabalho escravo e migrante na China, ou ainda de algum conflito africano sobre recursos minerais. Ao invés de empoderar alguma noção idealizada de sujeito, comunidade ou mesmo nação, ela demarca os limites e as condições do nosso entendimento sobre governança e sua relação com a produção, a fabricação e o design.Palavras-chave: Cultura Maker; Hardware de Fonte Aberta; Política e Design; Sul Global.ABSTRACT Maker culture defined as a set of Open Source Hardware (OSHW) tools (Weiss 2008; Mellis & Buechley 2011; Ames et al. 2014), DIY practices (Ratto & Boler 2014; Ames et al. 2014; Lindtner et al. 2016) and promises of digital, automated and distributed fabrication (Gershenfeld et al. 2004; Ratto & Ree 2012) or democratized science equipment (Pearce 2014; Pearce 2012) remains an ambiguous object of our recent political and design fantasies.  On one side, there is a surge of government and policy interests in the so called "maker movements" in the U.S., China, Singapore, Taiwan, and EU leading directly to the present nationalist calls for "Making (XYZ nation) great again". On the other, maker projects and activities (Arduino tinkering, building 3D printers,  setting up a DIYbio lab infrastructure)  remain niche, exploratory and private, even when they are part of the informal, transnational networks (Vertesi et al. 2011; Kaiying & Lindtner 2016), which I call "geek diplomacy" (Kera 2015).  Without clearly stating any local or transnational agenda, the DIY makers productively and creatively negotiate the various dichotomies between individualism and collectivism, local and global interests, nationalism and cosmopolitanism. They connect politics and design through "liminal," meaning individual and exploratory, experiences of prototyping and tinkering which differ greatly from the knowledge and skills acquisitions or prototyping common in the industrial or academic context. To explain this liminality in the maker culture, I extended Gabriella Coleman's (2012) pioneering work on the paradoxes of hacker (and open source software) movement. The decentralized and transnational networks of makers and hackers are examples of (technological) communitas and liminality (Turner 1969), which negotiate various conflicting goals and agenda behind making, technology and globalization.  The maker culture can serve isolationist and cosmopolitan agendas at the same time, even embrace the open source rhetoric while remaining partially patented, pirated and hybrid. It mobilizes the Global South hopes of low cost technologies while performing the Silicon Valley clichés and using migrant slave labor in China, but also African conflict minerals. Rather than empowering some idealized notion of the subject, community or even nation, it demarcates the limits and conditions of our understanding of governance and its relation to production, making, and design.Keywords: Maker Culture; Open Source Hardware; Politics and Design; Global South.


2019 ◽  
Author(s):  
Harrison Steel ◽  
Robert Habgood ◽  
Ciarán Kelly ◽  
Antonis Papachristodoulou

The precise characterisation and manipulation of in vivo biological systems is critical to their study.1 However, in many experimental frameworks this is made challenging by non-static environments during cell growth,2, 3 as well as variability introduced by manual sampling and measurement protocols.4 To address these challenges we present Chi.Bio, a parallelised open-source platform that offers a new experimental paradigm in which all measurement and control actions can be applied to a bulk culture in situ. In addition to continuous-culturing capabilities (turbidostat functionality, heating, stirring) it incorporates tunable light outputs of varying wavelengths and spectrometry. We demonstrate its application to studies of cell growth and biofilm formation, automated in silico control of optogenetic systems, and readout of multiple orthogonal fluorescent proteins. By combining capabilities from many laboratory tools into a single low-cost platform, Chi.Bio facilitates novel studies in synthetic, systems, and evolutionary biology, and broadens access to cutting-edge research capabilities.


2018 ◽  
Vol 373 (1758) ◽  
pp. 20170380 ◽  
Author(s):  
Matteo Cantarelli ◽  
Boris Marin ◽  
Adrian Quintana ◽  
Matt Earnshaw ◽  
Robert Court ◽  
...  

Geppetto is an open-source platform that provides generic middleware infrastructure for building both online and desktop tools for visualizing neuroscience models and data and managing simulations. Geppetto underpins a number of neuroscience applications, including Open Source Brain (OSB), Virtual Fly Brain (VFB), NEURON-UI and NetPyNE-UI. OSB is used by researchers to create and visualize computational neuroscience models described in NeuroML and simulate them through the browser. VFB is the reference hub for Drosophila melanogaster neural anatomy and imaging data including neuropil, segmented neurons, microscopy stacks and gene expression pattern data. Geppetto is also being used to build a new user interface for NEURON, a widely used neuronal simulation environment, and for NetPyNE, a Python package for network modelling using NEURON. Geppetto defines domain agnostic abstractions used by all these applications to represent their models and data and offers a set of modules and components to integrate, visualize and control simulations in a highly accessible way. The platform comprises a backend which can connect to external data sources, model repositories and simulators together with a highly customizable frontend. This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.


2018 ◽  
Author(s):  
Kalesh Sasidharan ◽  
Andrea S. Martinez-Vernon ◽  
Jing Chen ◽  
Tiantian Fu ◽  
Orkun S Soyer

ABSTRACTHigh-resolution data on microbial growth dynamics allow characterisation of microbial physiology, as well as optimisation of genetic alterations thereof. Such data are routinely collected using bench-top spectrophotometers or so-called plate readers. These equipments present several drawbacks: (i) measurements from different devices cannot be compared directly, (ii) proprietary nature of devices makes it difficult for standardisation methods to be developed across devices, and (iii) high costs limit access to devices, which can become a bottleneck for researchers, especially for those working with anaerobic organisms or at higher containment level laboratories. These limitations could be lifted, and data reproducibility improved, if the scientific community could adopt standardised, low-cost and open-source devices that can be built in-house. Here, we present such a device, MicrobeMeter, which is a do-it-yourself (DIY), simple, yet robust photometer with continuous data-logging capability. It is built using 3D-printing and open-source Arduino platform, combined with purpose-built electronic circuits. We show that MicrobeMeter displays linear relation between culture density and turbidity measurement for microbes from different phylogenetic domains. In addition, culture density estimated from MicrobeMeter measurements produced less variance compared against three commercial bench-top spectrophotometers, indicating that its measurements are less affected by the differences in cell types. We show the utility of MicrobeMeter, as a programmable wireless continuous measurement device, by collecting long-term growth dynamics up to 458 hours from aerobic and anaerobic cultures. We provide a full open-source description of MicrobeMeter and its implementation for faster adaptation and future development by the scientific community. The blueprints of the device, as well as ready-to-assemble kit versions are also made available throughwww.humanetechnologies.co.uk.


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