Democratising “Microscopi”: a 3D printed automated XYZT fluorescence imaging system for teaching, outreach and fieldwork

ABSTRACTCommercial fluorescence microscope stands and fully automated XYZt fluorescence imaging systems are generally beyond the limited budgets available for teaching and outreach. We have addressed this problem by developing “Microscopi”, an accessible, affordable, DIY automated imaging system that is built from 3D printed and commodity off-the-shelf hardware, including electro-mechanical, computer and optical components. Our design features automated sample navigation and image capture with a simple web-based graphical user interface, accessible with a tablet or other mobile device. The light path can easily be switched between different imaging modalities. The open source Python-based control software allows the hardware to be driven as an integrated imaging system. Furthermore, the microscope is fully customisable, which also enhances its value as a learning tool. Here, we describe the basic design and demonstrate imaging performance for a range of easily sourced specimens.HighlightsPortable, low cost, self-build from 3D printed and commodity componentsMultimodal imaging: bright field, dark field, pseudo-phase and fluorescenceAutomated XYZt imaging from a tablet or smartphone via a simple GUIWide ranging applications in teaching, outreach and fieldworkOpen source hardware and software design, allowing user modification

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Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

10.1101/194324 ◽

2017 ◽

Author(s):

Nuñez Isaac ◽

Matute Tamara ◽

Herrera Roberto ◽

Keymer Juan ◽

Marzullo Tim ◽

...

Keyword(s):

Genetic Resources ◽

Open Source ◽

Fluorescence Imaging ◽

Imaging System ◽

Fluorescent Proteins ◽

Low Cost ◽

Fluorescent Imaging ◽

Diverse Range ◽

Fluorescence Imaging System ◽

Open Source Hardware

AbstractThe advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential for STEM teaching in a high school environment, using it to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for STEM education, scientific research and bioengineering. All the resources developed here are available under open source licenses.

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Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

PLoS ONE ◽

10.1371/journal.pone.0187163 ◽

2017 ◽

Vol 12 (11) ◽

pp. e0187163 ◽

Cited By ~ 25

Author(s):

Isaac Nuñez ◽

Tamara Matute ◽

Roberto Herrera ◽

Juan Keymer ◽

Timothy Marzullo ◽

...

Keyword(s):

Open Source ◽

Fluorescence Imaging ◽

Imaging System ◽

Low Cost ◽

Teaching And Research ◽

Fluorescence Imaging System

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Democratising “Microscopi”: a 3D printed automated XYZT fluorescence imaging system for teaching, outreach and fieldwork

Wellcome Open Research ◽

10.12688/wellcomeopenres.16536.1 ◽

2021 ◽

Vol 6 ◽

pp. 63

Author(s):

Matthew Wincott ◽

Andrew Jefferson ◽

Ian M. Dobbie ◽

Martin J. Booth ◽

Ilan Davis ◽

...

Keyword(s):

Fluorescence Imaging ◽

Imaging System ◽

Imaging Systems ◽

Image Capture ◽

Optical Components ◽

Web Based ◽

Automated Imaging ◽

Fluorescence Imaging System ◽

3D Printed ◽

Imaging Performance

Commercial fluorescence microscope stands and fully automated XYZt fluorescence imaging systems are generally beyond the limited budgets available for teaching and outreach. We have addressed this problem by developing “Microscopi”, an accessible, affordable, DIY automated imaging system that is built from 3D printed and commodity off-the-shelf hardware, including electro-mechanical, computer and optical components. Our design features automated sample navigation and image capture with a simple web-based graphical user interface, accessible with a tablet or other mobile device. The light path can easily be switched between different imaging modalities. The open source Python-based control software allows the hardware to be driven as an integrated imaging system. Furthermore, the microscope is fully customisable, which also enhances its value as a learning tool. Here, we describe the basic design and demonstrate imaging performance for a range of easily sourced specimens.

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A low cost harmonically modulated chlorophyll fluorescence imaging system and frequency domain analysis of chlorophyll fluorescence

10.1109/metroagrifor52389.2021.9628797 ◽

2021 ◽

Author(s):

Dingle Jose

Keyword(s):

Chlorophyll Fluorescence ◽

Frequency Domain ◽

Fluorescence Imaging ◽

Imaging System ◽

Low Cost ◽

Domain Analysis ◽

Frequency Domain Analysis ◽

Chlorophyll Fluorescence Imaging ◽

Fluorescence Imaging System ◽

Modulated Chlorophyll Fluorescence

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A low-cost, compact, LED-based animal fluorescence imaging system

Biomedical Engineering and Environmental Engineering ◽

10.1201/b18419-20 ◽

2015 ◽

pp. 89-91

Author(s):

Yamin Song ◽

Chao Zhang ◽

Fuhong Cai

Keyword(s):

Fluorescence Imaging ◽

Imaging System ◽

Low Cost ◽

Fluorescence Imaging System

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

Optics Letters ◽

10.1364/ol.45.000260 ◽

2019 ◽

Vol 45 (1) ◽

pp. 260 ◽

Cited By ~ 7

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

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Clipping of an anterior spinal artery aneurysm using an endoscopic fluorescence imaging system for craniocervical junction epidural arteriovenous fistula: technical note

Journal of Neurosurgery Spine ◽

10.3171/2019.1.spine18983 ◽

2019 ◽

Vol 31 (2) ◽

pp. 279-284 ◽

Cited By ~ 2

Author(s):

Ahmed Mansour ◽

Toshiki Endo ◽

Tomoo Inoue ◽

Kenichi Sato ◽

Hidenori Endo ◽

...

Keyword(s):

Spinal Cord ◽

Arteriovenous Fistula ◽

Fluorescence Imaging ◽

Imaging System ◽

Artery Aneurysm ◽

Craniocervical Junction ◽

Anterior Spinal Artery ◽

Posterolateral Approach ◽

Fluorescence Imaging System ◽

Ventral Spinal Cord

The authors report the case of a 78-year-old man with a craniocervical junction epidural arteriovenous fistula who presented with subarachnoid hemorrhage from a ruptured anterior spinal artery (ASA) aneurysm. Because endovascular embolization was difficult, a posterolateral approach was chosen and a novel endoscopic fluorescence imaging system was utilized to clip the aneurysm. The fluorescence imaging system provided clear and magnified views of the ventral spinal cord simultaneously with the endoscope-integrated indocyanine green videoangiography, which helped safely obliterate the ASA aneurysm. With the aid of this novel imaging system, surgeons can appreciate and manipulate complex vascular pathologies of the ventral spinal cord through a posterolateral approach, even when the lesion is closely related to the ASA.

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Induction of Neural Plasticity Using a Low-Cost Open Source Brain-Computer Interface and a 3D-Printed Wrist Exoskeleton

Sensors ◽

10.3390/s21020572 ◽

2021 ◽

Vol 21 (2) ◽

pp. 572

Author(s):

Mads Jochumsen ◽

Taha Al Muhammadee Janjua ◽

Juan Carlos Arceo ◽

Jimmy Lauber ◽

Emilie Simoneau Buessinger ◽

...

Keyword(s):

Open Source ◽

Neural Plasticity ◽

Motor Evoked Potentials ◽

Low Cost ◽

True Positive Rate ◽

Positive Rate ◽

3D Printed ◽

Major Factors ◽

And Control ◽

Bci System

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.

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