scholarly journals A low-cost DIY device for high resolution, continuous measurement of microbial growth dynamics

2018 ◽  
Author(s):  
Kalesh Sasidharan ◽  
Andrea S. Martinez-Vernon ◽  
Jing Chen ◽  
Tiantian Fu ◽  
Orkun S Soyer
Keyword(s):  
High Resolution ◽  
Open Source ◽  
Scientific Community ◽  
Microbial Growth ◽  
Continuous Measurement ◽  
Low Cost ◽  
Growth Dynamics ◽  
Genetic Alterations ◽  
Data Logging ◽  
Culture Density

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.

scholarly journals Gloxinia—An Open-Source Sensing Platform to Monitor the Dynamic Responses of Plants

Sensors ◽  
2020 ◽  
Vol 20 (11) ◽  
pp. 3055
Author(s):  
Olivier Pieters ◽  
Tom De Swaef ◽  
Peter Lootens ◽  
Michiel Stock ◽  
Isabel Roldán-Ruiz ◽  
...  
Keyword(s):  
Open Source ◽  
Large Scale ◽  
Environmental Changes ◽  
Low Cost ◽  
Current Data ◽  
Dynamic Responses ◽  
Small Scale ◽  
Data Logging ◽  
Short Term ◽  
Sensing Platforms

The study of the dynamic responses of plants to short-term environmental changes is becoming increasingly important in basic plant science, phenotyping, breeding, crop management, and modelling. These short-term variations are crucial in plant adaptation to new environments and, consequently, in plant fitness and productivity. Scalable, versatile, accurate, and low-cost data-logging solutions are necessary to advance these fields and complement existing sensing platforms such as high-throughput phenotyping. However, current data logging and sensing platforms do not meet the requirements to monitor these responses. Therefore, a new modular data logging platform was designed, named Gloxinia. Different sensor boards are interconnected depending upon the needs, with the potential to scale to hundreds of sensors in a distributed sensor system. To demonstrate the architecture, two sensor boards were designed—one for single-ended measurements and one for lock-in amplifier based measurements, named Sylvatica and Planalta, respectively. To evaluate the performance of the system in small setups, a small-scale trial was conducted in a growth chamber. Expected plant dynamics were successfully captured, indicating proper operation of the system. Though a large scale trial was not performed, we expect the system to scale very well to larger setups. Additionally, the platform is open-source, enabling other users to easily build upon our work and perform application-specific optimisations.

scholarly journals HIGROTERM: An Open-Source and Low-Cost Temperature and Humidity Monitoring System for Laboratory Applications

Inventions ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 84
Author(s):  
Renan Rocha Ribeiro ◽  
Elton Bauer ◽  
Rodrigo Lameiras
Keyword(s):  
Open Source ◽  
Cost Reduction ◽  
Low Cost ◽  
Sensor Nodes ◽  
Real Problem ◽  
Data Logging ◽  
Bill Of Materials ◽  
Temperature And Humidity ◽  
The University ◽  
Humidity Monitoring

Low-cost electronics developed on easy-to-use prototyping platforms, such as Arduino, are becoming increasingly popular in various fields of science. This article presents an open-source and low-cost eight-channel data-logging system for temperature and humidity monitoring based on DHT22 (AM2302) sensors, named HIGROTERM. The system was designed to solve real needs of the Laboratory of Material Testing of the Department of Civil and Environmental Engineering at the University of Brasília. The system design, functionalities, hardware components, source code, bill of materials, assemblage and enclosure are thoroughly described to enable complete reproduction by the interested reader. The terminologies and instructions presented were simplified as much as possible to make it accessible to the greatest extent to researchers from different areas, especially those without electronics background. The data-acquisition system has an estimated total cost of USD 96.00, or USD 136.00 if eight sensor nodes are included, with a considerable margin for cost reduction. The authors expect that the HIGROTERM system may both be a valuable low-cost and customizable tool for the readers, as well a source of innovation and interest in low-cost electronics for real problem-solving in various fields of science.

scholarly journals One Metre Plus (1M+): A Multifunctional Open-Source Sensor for Bicycles Based on Raspberry Pi

Sensors ◽  
2021 ◽  
Vol 21 (17) ◽  
pp. 5812
Author(s):  
Andres Henao ◽  
Philippe Apparicio ◽  
David Maignan
Keyword(s):  
Knowledge Sharing ◽  
Open Source ◽  
Scientific Community ◽  
Low Cost ◽  
Video Recording ◽  
Raspberry Pi ◽  
Essential Tool ◽  
Geographical Position ◽  
Motorized Vehicles ◽  
Comparability Of Results

During the last decade, bicycles equipped with sensors became an essential tool for research, particularly for studies analyzing the lateral passing distance between motorized vehicles and bicycles. The objective of this article is to describe a low-cost open-source sensor called one metre plus (1m+) capable of measuring lateral passing distance, registering the geographical position of the cyclist, and video-recording the trip. The plans, codes, and schematic design are open and therefore easily accessible for the scientific community. This study describes in detail the conceptualization process, the characteristics of the device, and the materials from which they are made. The study also provides an evaluation of the product and describes the sensor’s functionalities and its field of application. The objective of this project is to democratize research and develop a platform/participative project that offers tools to researchers worldwide, in order to standardize knowledge sharing and facilitate the comparability of results in various contexts.

scholarly journals The Potential of Low-Cost UAVs and Open-Source Photogrammetry Software for High-Resolution Monitoring of Alpine Glaciers: A Case Study from the Kanderfirn (Swiss Alps)

Geosciences ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 356 ◽  
Author(s):  
Alexander R. Groos ◽  
Thalia J. Bertschinger ◽  
Céline M. Kummer ◽  
Sabrina Erlwein ◽  
Lukas Munz ◽  
...  
Keyword(s):  
High Resolution ◽  
Open Source ◽  
Low Cost ◽  
Swiss Alps ◽  
Glacier Surface ◽  
Proprietary Software ◽  
Open Hardware ◽  
Ground Control Points ◽  
Alpine Glaciers ◽  
Sensing Platforms

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.

Adapting a Low-Cost and Open-Source Commercial Pipetting Robot for Nanoliter Liquid Handling

2020 ◽  
pp. 247263032097359
Author(s):  
E. Enoch A. W. Councill ◽  
Nathanial B. Axtell ◽  
Thy Truong ◽  
Yiran Liang ◽  
Adam L. Aposhian ◽  
...  
Keyword(s):  
Open Source ◽  
Scientific Community ◽  
Low Cost ◽  
Mass Spectrometry Analysis ◽  
Liquid Chromatography Mass Spectrometry ◽  
Processing Efficiency ◽  
Spectrometry Analysis ◽  
Liquid Handling ◽  
Fluorescence Measurements ◽  
Volume Measurements

Low-volume liquid handling capabilities in bioanalytical workflows can dramatically improve sample processing efficiency and reduce reagent costs, yet many commercial nanoliter liquid handlers cost tens of thousands of dollars or more. We have successfully adapted a low-cost and open-source commercial pipetting robot, the Opentrons OT-1, to accurately aspirate and dispense nanoliter volumes. Based on fluorescence measurements, the modified OT-1 was able to reproducibly transfer 50 nL of water with less than 3% measurement error and 5% coefficient of variation (CV). For 15 nL transfers, the volume measurements indicated less than 4% error and 4% CV. We applied this platform to the preparation of low-nanogram proteomic samples for liquid chromatography–mass spectrometry analysis, demonstrating that the modified OT-1 is an effective platform for nanoliter liquid handling. At a total materials cost of less than $6000, including the commercial liquid handler and all modifications, this system is also far less expensive than other platforms with similar capabilities, placing automated nanoliter handling within reach of a far broader scientific community.

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

2022 ◽  
Author(s):  
Ana Rubio Denniss ◽  
Thomas E. Gorochowski ◽  
Sabine Hauert
Keyword(s):  
High Resolution ◽  
Open Source ◽  
De Novo ◽  
Low Cost ◽  
Local Interactions ◽  
Open Platform ◽  
The Individual ◽  
And Control

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]

scholarly journals A low-cost, open-source autonomous surface vehicle as a multipurpose waste stabilization pond monitoring platform

2018 ◽  
Vol 9 (1) ◽  
pp. 172-180
Author(s):  
A. Cuppens ◽  
G. Menesse ◽  
E. Caligaris ◽  
O. Marecos ◽  
G. Wyseure
Keyword(s):  
Open Source ◽  
Autonomous Navigation ◽  
Low Cost ◽  
Construction Materials ◽  
Working Environment ◽  
Monitoring Data ◽  
Data Logging ◽  
Data Logger ◽  
Autonomous Surface Vehicle ◽  
Waste Stabilization

Abstract Although waste stabilization ponds (WSPs) are widely used in developing countries, monitoring data on their operational performance are scarce. Traditional methods for monitoring in-pond conditions, i.e. conducting hand held measurements from a small boat or installing fixed sensor networks, are not straightforward to realize and create an unhealthy working environment for field workers. A promising technology for the safe and efficient collection of monitoring data is a compact autonomous surface vehicle (ASV), capable of autonomous navigation along a predefined trajectory based on geographic coordinates and measurements in different places and depths. In this practical paper, the development process, technical details and functional testing results of a low-cost ASV for WSP monitoring are presented. Commonly available construction materials and electronic components were used to ensure affordability and reparability. The access to online tutorials and peer-support was crucial for assembling the open-source autopilot and data logger. The ASV demonstrated satisfactory performance for both the autonomous navigation as well as the georeferenced data logging of measurements at a real-scale WSP in Paraguay. This study demonstrates how the adoption of open-source hardware and software offers the flexibility for the wastewater professionals to develop customized DIY solutions for specific monitoring applications and working environments.

scholarly journals A recipe for standards-based data sharing using open source software and low-cost electronics

2016 ◽  
Vol 18 (2) ◽  
pp. 185-197 ◽  
Author(s):  
Jeffrey M. Sadler ◽  
Daniel P. Ames ◽  
Rohit Khattar
Keyword(s):  
Information System ◽  
Open Source ◽  
Data Sharing ◽  
Low Cost ◽  
Transmission System ◽  
Environmental Data ◽  
Observation System ◽  
Design Development ◽  
Data Logging ◽  
Open Hardware

Environmental data are critical to understanding environmental phenomena, yet their consistent collection and curation can be cost-prohibitive. This paper describes a recipe for the design, development, and deployment of a low-cost environmental data logging and transmission system for environmental sensors and its connection to an open source data-sharing network. The hardware is built using several low-cost, open-source, mass-produced components. The system automatically ingests data into HydroServer, a standards-based server in the open source hydrologic information system (HIS) created by the Consortium of Universities for the Advancement of Hydrologic Sciences Inc. (CUAHSI). By publishing data in this way, they are discoverable through the geographic information system (GIS)-based CUAHSI tools, HydroDesktop and HydroShare. In addition, because they follow WaterML encoding, open hardware data stored in the HIS can be included in international catalog such as the global earth observation system of system catalog. A recipe for building the system is provided. Multiple deployments used to test proof-of-concept of the system are described and their results are given. Ease of deployment and reliability of the logging and transmission system is also addressed.

scholarly journals PI-Plat: a high-resolution image-based 3D reconstruction method to estimate growth dynamics of rice inflorescence traits

Plant Methods ◽  
2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Jaspreet Sandhu ◽  
Feiyu Zhu ◽  
Puneet Paul ◽  
Tian Gao ◽  
Balpreet K. Dhatt ◽  
...  
Keyword(s):  
High Resolution ◽  
3D Reconstruction ◽  
Low Cost ◽  
Crop Improvement ◽  
Growth Dynamics ◽  
Superior Performance ◽  
Plant Phenotyping ◽  
Reconstruction Method ◽  
Color Intensity ◽  
Non Destructive

Abstract Background Recent advances in image-based plant phenotyping have improved our capability to study vegetative stage growth dynamics. However, more complex agronomic traits such as inflorescence architecture (IA), which predominantly contributes to grain crop yield are more challenging to quantify and hence are relatively less explored. Previous efforts to estimate inflorescence-related traits using image-based phenotyping have been limited to destructive end-point measurements. Development of non-destructive inflorescence phenotyping platforms could accelerate the discovery of the phenotypic variation with respect to inflorescence dynamics and mapping of the underlying genes regulating critical yield components. Results The major objective of this study is to evaluate post-fertilization development and growth dynamics of inflorescence at high spatial and temporal resolution in rice. For this, we developed the Panicle Imaging Platform (PI-Plat) to comprehend multi-dimensional features of IA in a non-destructive manner. We used 11 rice genotypes to capture multi-view images of primary panicle on weekly basis after the fertilization. These images were used to reconstruct a 3D point cloud of the panicle, which enabled us to extract digital traits such as voxel count and color intensity. We found that the voxel count of developing panicles is positively correlated with seed number and weight at maturity. The voxel count from developing panicles projected overall volumes that increased during the grain filling phase, wherein quantification of color intensity estimated the rate of panicle maturation. Our 3D based phenotyping solution showed superior performance compared to conventional 2D based approaches. Conclusions For harnessing the potential of the existing genetic resources, we need a comprehensive understanding of the genotype-to-phenotype relationship. Relatively low-cost sequencing platforms have facilitated high-throughput genotyping, while phenotyping, especially for complex traits, has posed major challenges for crop improvement. PI-Plat offers a low cost and high-resolution platform to phenotype inflorescence-related traits using 3D reconstruction-based approach. Further, the non-destructive nature of the platform facilitates analyses of the same panicle at multiple developmental time points, which can be utilized to explore the genetic variation for dynamic inflorescence traits in cereals.

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