scholarly journals An Open-Source Framework for Automated High-Throughput Cell Biology Experiments

2021 ◽  
Vol 9 ◽  
Author(s):  
Pavel Katunin ◽  
Jianbo Zhou ◽  
Ola M. Shehata ◽  
Andrew A. Peden ◽  
Ashley Cadby ◽  
...  
Keyword(s):  
Open Source ◽  
High Throughput ◽  
Cell Biology ◽  
Large Scale ◽  
Low Cost ◽  
Fluorescent Labeling ◽  
Open Source Framework ◽  
Open Source Hardware ◽  
High Degree ◽  
Data Analysis Methods

Modern data analysis methods, such as optimization algorithms or deep learning have been successfully applied to a number of biotechnological and medical questions. For these methods to be efficient, a large number of high-quality and reproducible experiments needs to be conducted, requiring a high degree of automation. Here, we present an open-source hardware and low-cost framework that allows for automatic high-throughput generation of large amounts of cell biology data. Our design consists of an epifluorescent microscope with automated XY stage for moving a multiwell plate containing cells and a perfusion manifold allowing programmed application of up to eight different solutions. Our system is very flexible and can be adapted easily for individual experimental needs. To demonstrate the utility of the system, we have used it to perform high-throughput Ca2+ imaging and large-scale fluorescent labeling experiments.

scholarly journals An open-source experimental framework for automation of cell biology experiments

2020 ◽  
Author(s):  
Pavel Katunin ◽  
Ashley Cadby ◽  
Anton Nikolaev
Keyword(s):  
Open Source ◽  
Cell Biology ◽  
Biological Data ◽  
List Type ◽  
Fluorescent Reporters ◽  
Fluorescent Microscope ◽  
Treatment Conditions ◽  
Key Points ◽  
Open Source Hardware ◽  
High Degree

AbstractModern data analysis methods, such as deep learning, have been successfully applied to a number of biological and medical questions. For these methods to be efficient, a large number of high quality experiments need to be conducted, which requires a high degree of automation. Here we report an open-source hardware that allows for automatic high-throughput generation of large amounts of biological data. The hardware consists of an automatic XY-stage for moving multiwell plates containing growing cells; a perfusion manifold allowing application (perfusion) of up to 8 different solutions; and a small epifluorescent microscope. It is extremely cheap (£300 without and £2500 with a fluorescent microscope) and can be quickly customised for individual experimental needs.Key points- We present an open source framework for automation of cell biology experiments- The framework consists of an XY platform, application of up to 8 solutions and a small epifluorescent microscope- Very cheap (£300 without a fluorescent microscope and £2500 with a fluorescent microscope), customisable, 3D printable- Can be used in a variety of biological applications such as imaging of fluorescent reporters, optimisation of treatment conditions and immuno-labelling

scholarly journals OpenWSI: a low-cost, high-throughput whole slide imaging system via single-frame autofocusing and open-source hardware

2019 ◽  
Vol 45 (1) ◽  
pp. 260 ◽  
Author(s):  
Chengfei Guo ◽  
Zichao Bian ◽  
Shaowei Jiang ◽  
Michael Murphy ◽  
Jiakai Zhu ◽  
...  
Keyword(s):  
Open Source ◽  
High Throughput ◽  
Imaging System ◽  
Low Cost ◽  
Whole Slide Imaging ◽  
Single Frame ◽  
Open Source Hardware

scholarly journals PRISMS-Fatigue computational framework for fatigue analysis in polycrystalline metals and alloys

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Mohammadreza Yaghoobi ◽  
Krzysztof S. Stopka ◽  
Aaditya Lakshmanan ◽  
Veera Sundararaghavan ◽  
John E. Allison ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Metals And Alloys ◽  
Analysis Tool ◽  
Computational Framework ◽  
Crystal Plasticity Finite Element ◽  
Polycrystalline Metals ◽  
Simulation Based ◽  
Open Source Framework

AbstractThe PRISMS-Fatigue open-source framework for simulation-based analysis of microstructural influences on fatigue resistance for polycrystalline metals and alloys is presented here. The framework uses the crystal plasticity finite element method as its microstructure analysis tool and provides a highly efficient, scalable, flexible, and easy-to-use ICME community platform. The PRISMS-Fatigue framework is linked to different open-source software to instantiate microstructures, compute the material response, and assess fatigue indicator parameters. The performance of PRISMS-Fatigue is benchmarked against a similar framework implemented using ABAQUS. Results indicate that the multilevel parallelism scheme of PRISMS-Fatigue is more efficient and scalable than ABAQUS for large-scale fatigue simulations. The performance and flexibility of this framework is demonstrated with various examples that assess the driving force for fatigue crack formation of microstructures with different crystallographic textures, grain morphologies, and grain numbers, and under different multiaxial strain states, strain magnitudes, and boundary conditions.

scholarly journals Computer Numerically Controlled Drawing Robot Based on Computer-Aided Design

2021 ◽  
Author(s):  
Antor Mahamudul Hashan ◽  
Abdullah Haidari ◽  
Srishti Saha ◽  
Titas Paul
Keyword(s):  
Open Source ◽  
Computer Aided Design ◽  
Low Cost ◽  
Rapid Development ◽  
Main Idea ◽  
Numerical Control ◽  
Computer Aided ◽  
Complex Circuits ◽  
Open Source Hardware ◽  
Aided Design

Due to the rapid development of technology, the use of numerically controlled machines in the industry is increasing. The main idea behind this paper is computer-aided design (CAD) based low-cost computer numerical control 2D drawing robot that can accurately draw complex circuits, diagrams, logos, etc. The system is created using open-source hardware and software, which makes it available at a low cost. The open-source LibreCAD application has been used for computer-aided design. Geometric data of a CAD model is converted to coordinate points using the python-based F-Engrave application. This system uses the Arduino UNO board as a signal generator of the universal g-code sender without compromising the performance. The proposed drawing robot is designed as a low-cost robot for educational purposes and aims to increase the student's interest in robotics and computer-aided design (CAD) skills to the next level. The drawing robot structure has been developed, and it meets the requirements of low cost with satisfactory experimental results.

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 micrIO: an open-source autosampler and fraction collector for automated microfluidic input–output

Lab on a Chip ◽  
2020 ◽  
Vol 20 (1) ◽  
pp. 93-106 ◽  
Author(s):  
Scott A. Longwell ◽  
Polly M. Fordyce
Keyword(s):  
Open Source ◽  
Low Cost ◽  
Microfluidic Devices ◽  
Input Output ◽  
Fraction Collector ◽  
Open Source Hardware ◽  
Multiwell Plates

MicrIO is a low-cost, open-source hardware and software solution for automated sample input/output, bridging the gap between microfluidic devices and standard multiwell plates.

Web-Based Large-Scale 3D-Geovisualisation Using WebGL

2012 ◽  
Vol 1 (3) ◽  
pp. 16-25 ◽  
Author(s):  
Martin Christen ◽  
Stephan Nebiker ◽  
Benjamin Loesch
Keyword(s):  
Open Source ◽  
Broad Spectrum ◽  
Large Scale ◽  
Interactive Visualization ◽  
Web Browsers ◽  
Web Based ◽  
Virtual Globe ◽  
Open Source Framework ◽  
The Creation

In this paper, the authors present the OpenWebGlobe project (http://www.openwebglobe.org). The authors also discuss the OpenWebGlobe SDK. OpenWebGlobe SDK is an open source framework for creating massive 3D virtual globe environments and interactively exploiting them in web browsers using HTML5 and WebGL, allowing for the creation of large scale virtual 3D globes with detailed contents and their interactive visualization directly within a broad spectrum of Web browsers.

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