scholarly journals OptiJ: Open-source optical projection tomography of large organ samples

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Pedro P. Vallejo Ramirez ◽  
Joseph Zammit ◽  
Oliver Vanderpoorten ◽  
Fergus Riche ◽  
Francois-Xavier Blé ◽  
...  
Keyword(s):  
Open Source ◽  
Low Cost ◽  
Three Dimensional ◽  
Optical Projection Tomography ◽  
Optical Components ◽  
Adult Mice ◽  
Optical Projection ◽  
Set Up ◽  
Imagej Plugin ◽  
Lung Lobes

Abstract The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.

scholarly journals OptiJ: Open-source optical projection tomography of large organ samples

2019 ◽  
Author(s):  
Pedro P. Vallejo Ramirez ◽  
Joseph Zammit ◽  
Oliver Vanderpoorten ◽  
Fergus Riche ◽  
François-Xavier Blé ◽  
...  
Keyword(s):  
Open Source ◽  
Low Cost ◽  
Three Dimensional ◽  
Optical Projection Tomography ◽  
Optical Components ◽  
Adult Mice ◽  
Optical Projection ◽  
Set Up ◽  
Imagej Plugin ◽  
Lung Lobes

The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 μm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.

Optimum Design for the Frame of Open Type Abrasive Flow Polish Machine

2012 ◽  
Vol 497 ◽  
pp. 89-93
Author(s):  
Liang Liang Yuan ◽  
Ke Hua Zhang ◽  
Li Min
Keyword(s):  
Finite Element ◽  
Natural Frequency ◽  
Finite Element Methods ◽  
Optimization Design ◽  
Low Cost ◽  
Three Dimensional ◽  
Force Model ◽  
Optimization Analysis ◽  
Open Type ◽  
Set Up

In order to process heterotype hole of workpiece precisely, an open abrasive flow polish machine is designed, and the optimization design of machine frame is done for low cost. Firstly, basing on the parameters designed with traditional ways, three-dimensional force model is set up with the soft of SolidWorks. Secondly, the statics and modal analysis for machine body have been done in Finite element methods (FEM), and then the optimization analysis of machine frame has been done. At last, the model of rebuild machine frame has been built. Result shows that the deformation angle value of machine frame increased from 0.72′ to 1.001′, the natural frequency of the machine decreased from 75.549 Hz to 62.262 Hz, the weight of machine decreased by 74.178 Kg after optimization. It meets the strength, stiffness and angel stiffness requirement of machine, reduces the weight and cost of machine.

scholarly journals 3-D Printable Polymer Pelletizer Chopper for Fused Granular Fabrication-Based Additive Manufacturing

Inventions ◽  
2018 ◽  
Vol 3 (4) ◽  
pp. 78 ◽  
Author(s):  
Aubrey Woern ◽  
Joshua Pearce
Keyword(s):  
Additive Manufacturing ◽  
Open Source ◽  
Low Cost ◽  
Three Dimensional ◽  
High Tolerance ◽  
Entire Process ◽  
Composite Fabrication ◽  
The Us ◽  
Color Mixing ◽  
Returns On Investment

Although distributed additive manufacturing can provide high returns on investment, the current markup on commercial filament over base polymers limits deployment. These cost barriers can be surmounted by eliminating the entire process of fusing filament by three-dimensional (3-D) printing products directly from polymer granules. Fused granular fabrication (FGF) (or fused particle fabrication (FPF)) is being held back in part by the accessibility of low-cost pelletizers and choppers. An open-source 3-D printable invention disclosed here allows for precisely controlled pelletizing of both single thermopolymers as well as composites for 3-D printing. The system is designed, built, and tested for its ability to provide high-tolerance thermopolymer pellets with a number of sizes capable of being used in an FGF printer. In addition, the chopping pelletizer is tested for its ability to chop multi-materials simultaneously for color mixing and composite fabrication as well as precise fractional measuring back to filament. The US$185 open-source 3-D printable pelletizer chopper system was successfully fabricated and has a 0.5 kg/h throughput with one motor, and 1.0 kg/h throughput with two motors using only 0.24 kWh/kg during the chopping process. Pellets were successfully printed directly via FGF as well as indirectly after being converted into high-tolerance filament in a recyclebot.

scholarly journals The Flexiscope: a low cost, flexible, convertible and modular microscope with automated scanning and micromanipulation

2020 ◽  
Vol 7 (3) ◽  
pp. 191949 ◽  
Author(s):  
Amy Courtney ◽  
Luke M. Alvey ◽  
George O. T. Merces ◽  
Niamh Burke ◽  
Mark Pickering
Keyword(s):  
Experimental Design ◽  
High Performance ◽  
Low Cost ◽  
Three Dimensional ◽  
Cost Savings ◽  
Fluorescent Imaging ◽  
Multiple Roles ◽  
Flexible Work ◽  
Optical Components ◽  
Automated Scanning

With technologies rapidly evolving, many research institutions are now opting to invest in costly, high-quality, specialized microscopes which are shared by many researchers. As a consequence, the user may not have the ability to adapt a microscope to their specific needs and limitations in experimental design are introduced. A flexible work-horse microscopy system is a valuable tool in any laboratory to meet the diverse needs of a research team and promote innovation in experimental design. We have developed the Flexiscope; a multi-functional, adaptable, efficient and high-performance microscopy/electrophysiology system for everyday applications in a neurobiology laboratory. The core optical components are relatively constant in the three configurations described here: an upright configuration, an inverted configuration and an upright/electrophysiology configuration. We have provided a comprehensive description of the Flexiscope. We show that this method is capable of oblique infrared illumination imaging, multi-channel fluorescent imaging and automated three-dimensional scanning of larger specimens. Image quality is conserved across the three configurations of the microscope, and conversion between configurations is possible quickly and easily, while the motion control system can be repurposed to allow sub-micrometre computer-controlled micromanipulation. The Flexiscope provides similar performance and usability to commercially available systems. However, as it can be easily reconfigured for multiple roles, it can remove the need to purchase multiple microscopes, giving significant cost savings. The modular reconfigurable nature allows the user to customize the system to their specific needs and adapt/upgrade the system as challenges arise, without requiring specialized technical skills.

scholarly journals Software-Based Three-Dimensional Deconvolution Microscopy of Cytoskeletal Proteins in Cultured Fibroblast Using Open-Source Software and Open Hardware

2019 ◽  
Vol 5 (12) ◽  
pp. 88
Author(s):  
Kazuo Katoh
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Laser Scanning ◽  
Low Cost ◽  
Three Dimensional ◽  
Cytoskeletal Proteins ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Actual Measurement ◽  
Open Hardware

As conventional fluorescence microscopy and confocal laser scanning microscopy generally produce images with blurring at the upper and lower planes along the z-axis due to non-focal plane image information, the observation of biological images requires “deconvolution.” Therefore, a microscope system’s individual blur function (point spread function) is determined theoretically or by actual measurement of microbeads and processed mathematically to reduce noise and eliminate blurring as much as possible. Here the author describes the use of open-source software and open hardware design to build a deconvolution microscope at low cost, using readily available software and hardware. The advantage of this method is its cost-effectiveness and ability to construct a microscope system using commercially available optical components and open-source software. Although this system does not utilize expensive equipment, such as confocal and total internal reflection fluorescence microscopes, decent images can be obtained even without previous experience in electronics and optics.

scholarly journals LOW-COST SIMULATOR ASSEMBLY FOR 3-DIMENSIONAL VIDEOSURGERY TRAINING

2018 ◽  
Vol 31 (3) ◽  
Author(s):  
Carlos Magno Queiroz da CUNHA ◽  
Douglas Marques Ferreira de LIMA ◽  
Francisco Julimar Correia de MENEZES
Keyword(s):  
Low Cost ◽  
Three Dimensional ◽  
Skills Training ◽  
Surgical Skills ◽  
3D Video ◽  
Training Methods ◽  
3 Dimensional ◽  
Set Up ◽  
Undergraduate Programs ◽  
Advanced Courses

ABSTRACT Background: Three-dimensional videosurgery is already a reality worldwide. The trainee program for this procedure should be done initially and preferably in simulators. Aim: Assemble low-cost simulator for three-dimensional videosurgery training. Methods: The simulator presented here was mounted in two parts, base and glasses. After, several stations can be inserted into the simulator for skills training in videosurgery. Results: It was possible to set up three dimensional (3D) video simulations with low cost. It has proved to be easy to assemble and allows the training surgeon of various video surgical skills. Conclusion: This equipment may be used in undergraduate programs and advanced courses for residents and surgeons. The acrylic box allows the visualization of the task executed by the tutor and even by other experienced students.

scholarly journals Optical Projection Tomography Using a Commercial Microfluidic System

Micromachines ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 293
Author(s):  
Wenhao Du ◽  
Cheng Fei ◽  
Junliang Liu ◽  
Yongfu Li ◽  
Zhaojun Liu ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Numerical Aperture ◽  
Microfluidic System ◽  
Depth Of Field ◽  
Objective Lens ◽  
Flow Mode ◽  
Wide Field ◽  
Optical Projection Tomography ◽  
Microfluidic Systems ◽  
Optical Projection

Optical projection tomography (OPT) is the direct optical equivalent of X-ray computed tomography (CT). To obtain a larger depth of field, traditional OPT usually decreases the numerical aperture (NA) of the objective lens to decrease the resolution of the image. So, there is a trade-off between sample size and resolution. Commercial microfluidic systems can observe a sample in flow mode. In this paper, an OPT instrument is constructed to observe samples. The OPT instrument is combined with commercial microfluidic systems to obtain a three-dimensional and time (3D + T)/four-dimensional (4D) video of the sample. “Focal plane scanning” is also used to increase the images’ depth of field. A series of two-dimensional (2D) images in different focal planes was observed and compared with images simulated using our program. Our work dynamically monitors 3D OPT images. Commercial microfluidic systems simulate blood flow, which has potential application in blood monitoring and intelligent drug delivery platforms. We design an OPT adaptor to perform OPT on a commercial wide-field inverted microscope (Olympusix81). Images in different focal planes are observed and analyzed. Using a commercial microfluidic system, a video is also acquired to record motion pictures of samples at different flow rates. To our knowledge, this is the first time an OPT setup has been combined with a microfluidic system.

Sleeve gastrectomy, but not duodenojejunostomy, preserves total beta-cell mass in Goto-Kakizaki rats evaluated by three-dimensional optical projection tomography

2015 ◽  
Vol 30 (2) ◽  
pp. 532-542 ◽  
Author(s):  
Eivind Grong ◽  
Bård Kulseng ◽  
Ingerid Brænne Arbo ◽  
Christoffer Nord ◽  
Maria Eriksson ◽  
...  
Keyword(s):  
Sleeve Gastrectomy ◽  
Beta Cell ◽  
Cell Mass ◽  
Three Dimensional ◽  
Beta Cell Mass ◽  
Optical Projection Tomography ◽  
Optical Projection ◽  
Total Beta

scholarly journals High throughput transmission optical projection tomography using low cost graphics processing unit

2009 ◽  
Vol 17 (25) ◽  
pp. 22320 ◽  
Author(s):  
Claudio Vinegoni ◽  
Lyuba Fexon ◽  
Paolo Fumene Feruglio ◽  
Misha Pivovarov ◽  
Jose-Luiz Figueiredo ◽  
...  
Keyword(s):  
High Throughput ◽  
Graphics Processing Unit ◽  
Low Cost ◽  
Processing Unit ◽  
Optical Projection Tomography ◽  
Optical Projection ◽  
Graphics Processing

scholarly journals Open source modules for tracking animal behavior and closed-loop stimulation based on Open Ephys and Bonsai

2018 ◽  
Author(s):  
Alessio Paolo Buccino ◽  
Mikkel Elle Lepperød ◽  
Svenn-Arne Dragly ◽  
Philipp Häfliger ◽  
Marianne Fyhn ◽  
...  
Keyword(s):  
Open Source ◽  
Real Time ◽  
Closed Loop ◽  
Low Cost ◽  
Data Formats ◽  
Behavioral Tracking ◽  
Real Time Tracking ◽  
Set Up ◽  
And Behavior ◽  
Closed Loop Stimulation

AbstractObjectiveA major goal in systems neuroscience is to determine the causal relationship between neural activity and behavior. To this end, methods that combine monitoring neural activity, behavioral tracking, and targeted manipulation of neurons in closed-loop are powerful tools. However, commercial systems that allow these types of experiments are usually expensive and rely on non-standardized data formats and proprietary software which may hinder user-modifications for specific needs. In order to promote reproducibility and data-sharing in science, transparent software and standardized data formats are an advantage. Here, we present an open source, low-cost, adaptable, and easy to set-up system for combined behavioral tracking, electrophysiology and closed-loop stimulation.ApproachBased on the Open Ephys system (www.open-ephys.org) we developed multiple modules to include real-time tracking and behavior-based closed-loop stimulation. We describe the equipment and provide a step-by-step guide to set up the system. Combining the open source software Bonsai (bonsai-rx.org) for analyzing camera images in real time with the newly developed modules in Open Ephys, we acquire position information, visualize tracking, and perform tracking-based closed-loop stimulation experiments. To analyze the acquired data we provide an open source file reading package in Python.Main resultsThe system robustly visualizes real-time tracking and reliably recovers tracking information recorded from a range of sampling frequencies (30-1000Hz). We combined electrophysiology with the newly-developed tracking modules in Open Ephys to record place cell and grid cell activity in the hippocampus and in the medial entorhinal cortex, respectively. Moreover, we present a case in which we used the system for closed-loop optogenetic stimulation of entorhinal grid cells.SignificanceExpanding the Open Ephys system to include animal tracking and behavior-based closed-loop stimulation extends the availability of high-quality, low-cost experimental setup within standardized data formats serving the neuroscience community.

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