Difference between revisions of "Team:Cambridge-JIC/Design"

Problem Statement

Microscopy has had a major impact on science and society since its invention in the 1600s, revealing a previously undiscovered world and leading to an explosion in ideas to the future possibilities of such imaging systems. Despite this, more that 400 years later, microscopy is still a tool reserved for those with the means to invest. Microscopes for tens of thousands of pounds can be found in professional research labs being used for some fantastic, but generally publicly removed, work. We want this to change: making microscopy a tool accessible to anyone, no matter their occupation or what they wish to do with it.

Microscopy has become a fundamental, quantitative measurement tool in the field of synthetic biology. Synthetic biology is another scientific area that has been poorly communicated to the public, with their knowledge of the field and its applications being mainly negative. We aim to increase the public’s awareness of synthetic biology using a previously inaccessible research tool to highlight the importance of developement in science.

What are the current options?

In fig. 1 it is possible to see that each microscope has several attributes making it highly creditable. It is well known that commercial microscopes are able to produce immensely high quality images and will always be indispensable, lab research tools. However, it can also be seen that they have several undesirable qualities, decreasing their appeal to some users. For comparison we have the low cost, light weight and easy to use newer alternatives. They have the traits that we wish could be seen in conventional microscopes. These microscopes are created to thoroughly fulfill their one objective: The FoldScope (a several use educational tool and potential diagnostic tool); The FlyPi (for fluorescence macro-imaging of Drosophila flies) and the smartphone microscope (for low resolution imaging using your phone). OpenScope aims to fill a gap in the field, competing to match not quality, but the use of a conventional microscope.

Social Impact

We can see OpenScope have huge impact in many areas of society.

Education: Bright field microscopes can be found in most secondary school and some primary schools. Fluorescence microscopes are far outside the budget of the school schools. The problem with the public’s knowledge and perception of the synthetic biology field has been previously highlighted. If synthetic biology could be taught to children from a young age through the use of fluorescence microscopy we could alleviate this lack of understanding in future generations. At the Outreach Event the teacher was very keen to have this implemented in the school curriculum. OpenScope allows this to be a possibility. It also allows for integrated learning across many STEM subjects, microscope assembly projects and interactive homework exercises.

Research: Most research labs can afford a commercial fluorescence microscope, but budget constraints mean there is usually only one for the whole lab. Time on it may have to be booked, decreasing productivity considerably. OpenScope is a tool which can be used alongside the commercial microscopes to enable researchers to quickly image new samples, or perform such things as time-lapse imaging. OpenScopes is compact, allowing it to be placed within fume hoods or incubators. With an OpenScope smaller research labs will have the means to compete with research in acclaimed labs.

On the move: OpenScope is light weight and can be battery powered. This makes it ideal for fieldwork and travelling. It can also be controlled by remote access, allowing you to check on your samples in the lab from the comfort of your home.

Developing countries: It is hoped that OpenScope will be in the budget of small labs in developing countries. Its ease of assembly and portability will allow parts to be manufactured in the UK and sent to wherever they are needed to be build.

Integrated Design

Integration of Pre-Existing Microscope

Our design incorporates a number for key features that were developed as part of a contemporary at the University of Cambridge [1]. The PiScope is an inverted brightfield microscope that uses 3D printed parts in a flexure-based mechanism for sample translation.

Although OpenScope is an upright microscope, it makes use of plastic flexure in the microscope stage to give fine control of translation along the x- and y-axis. In this respect, it takes ideas developed elsewhere and develops them in the context of a different microscope type. While the PiScope [1] uses the same mechanism for z-axis translation, this was seen as incompatible with the necessity for modularity in OpenScope. For this reason, OpenScope instead uses a more simple screw-based system for focusing up and down. For analysis of these systems, see the Specs page.

OSH and collaborative improvement

Based on research carried out as part of our Human Practices project, it was decided that the most appropriate license for OpenScope’s documentation would be a Copyleft license. In using a Creative Commons Attribution-ShareAlike license, OpenScope’s designs have been made available to the community with the assurance that they, along with any derivative work, will remain accessible into the future. Importantly, this gives the community of ‘makers’ the freedom to modify, improve and re-distribute our designs.

Over time, OpenScope has the potential to evolve and even diversify into different projects. Scientists and enthusiasts alike will be able to tailor both the hardware and software to their specific needs. Essentially, the OpenScope project can continue long after the iGEM competition has finished.

Desktop CNC integration

When considering Stretch Goals for our project, it was recognised that removing the chassis and replacing it with the headpiece of a desktop CNC machine could provide a sample screening system. This was tested in the lab, using the Raspberry Pi camera for macro imaging. As a proof of principle, this demonstrated that because of its modular and digital nature, the potential for developing the OpenScope project in different directions is huge.

Modularity

OpenScope makes use of two key open-source hardware components, namely the Arduino [2] (a microprocessor) and the Raspberry Pi [3]. The versatility and the well-developed community of ‘makers’ associated with these components are directly transferable to OpenScope itself. In addition, they represent a standardised aspect of our project that is compatible with an existing (and rapidly growing) array of hardware projects and scientific equipment. Examples include Arduino-based centrifuges and spectrometers [4] as well as the RepRap 3D printer [5].

The Raspberry Pi makes OpenScope entirely digital, letting the user control and program it using specifically designed software. New software can easily be added to the arsenal of features already available, and the existing software can be modified and improved according to the Copyleft license it’s under.

ImageJ is a widely-used microscopy software that already has features such as cell-counting algorithms and annotation. To make OpenScope easy to integrate into standard scientific experiments, a plug-in for ImageJ has been developed that enables the user to implement programs to process images captured directly from OpenScope. In short, the transition between OpenScope and this standard laboratory software is seamless.

Environmental Impact

The bulk of the microscope is polylactic acid (PLA). PLA is a fully biodegradable polymer, derived from sugarcane. Its thermoplastic nature means it has the potential for being recycled into many products at the end of the microscope's life¹. The other main components are the printed circuit boards used in the Raspberry Pi and Arduino. These contain silicon chips and other components such as lead, cadmium and mercury. These can be hazardous in the environment if not recycled or disposed of safely ².

This gives a brief overview of environmental considerations associated with OpenScope. However, we wished to gain a more in depth understanding of environmental impacts, both for us and others using the microscope. A full life cycle analysis was carried out using using the Eco Audit tool on the CES Selector Program³. The program allows for the energy use in MJ and carbon emissions in kg to be calculated for the product over its lifetime. The Eco Audit tool calculates these by taking into consideration the materials and material processing used, the use of the product, the power consumption (calculations for power consumption are given here) and any transportation involved.

Assumptions

• Materials and Processing: For each part of the microscope only the main materials, making up the majority of the part, were considered. Materials and manufacturing processes were collated from online and are accurate to the best of our knowledge. There is not an option on the tool for 3D printing as a materials process and so from the chassis said to be made by polymer moulding, the most similar process.

• Transportation: All parts for the microscope are being sourced locally, many parts can be bought in bulk and it would assume the only transportation would be by light goods vehicles, travelling across England.

• Use: We assumed the average person would use our microscope 4 days a week and use it for 2 hours each of these days. It was also assumed that the microscope would have a lifetime of 1 year.

• Disposal: All materials that could be were recycled, the rest were disposed of in landfill

Most energy is produced from the materials used to make the microscope, at approximately 10 times that of the use energy. Some energy can be regained at the end of the microscope's life if the materials that can be are recycled.

Useful Software

Below is a list of software programs that we have found useful for developing open-source hardware, supplemented with other commonly used programs:

1. OpenSCAD – a free, open-source, parametric CAD platform used to design 3D objects for printing (available from here)

2. Tracker – a free, open-source, video analysis and modelling tool. Used to track moving objects in videos and extract data (available from here)

3. Cura 3D – a free, open-source 3D printer interface from Ultimaker. Used to control printer settings (available from here)

4. Fiji - a free, open-source image processing and analysis platform. Particularly useful for microscopy (available from here)

5. Inkscape – a free, open-source vector graphics package. Extremely useful for 2D design followed by linear extrusion (available from here)

6. DesignSpark – a free electronics design software for PCB prototyping. Has an online library of over 80,000 parts (available from here)

7. Scribus – a free, open-source graphics software. Particularly useful for publishing (available from here)

8. Python – a free, open-source, programming language that allowed us to put together software quickly

9. Nginx – A FOSS lightweight web server on top of which we built our web interfaces.

10. OpenCV – A FOSS released under a BSD license that provides a library for image processing software (available from here)

For a detailed list of free, open-source software programs available, look here.

References

[1] Bowman, R., Sharkey, J., Kabla, A., Baumberg, J. and Foo, D. (2015). A one-piece 3D printed microscope and flexure translation stage. arXiv.

[2] Arduino.cc, (2015). Arduino - Home. https://www.arduino.cc/ [Accessed 18 Sep. 2015].

[3] Raspberry Pi, (2015). Raspberry Pi - Teach, Learn, and Make with Raspberry Pi.https://www.raspberrypi.org/ [Accessed 18 Sep. 2015].

[4] Pearce, J. (2014). Open-source lab. Amsterdam [u.a.]: Elsevier.

[5] Wittbrodt, B., Glover, A., Laureto, J., Anzalone, G., Oppliger, D., Irwin, J. and Pearce, J. (2013). Life-cycle economic analysis of distributed manufacturing with open-source 3-D printers.Mechatronics, 23(6), pp.713-726.

[1] Yutaka Tokiwa; Buenaventurada P. Calabia; Charles U. Ugwu; Seiichi Aiba, "Biodegradability of Plastics", 2009, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2769161/.

[2] Lucy McAllister, "The Human and Environmental Effects of E-Waste", 2015, http://www.prb.org/Publications/Articles/2013/e-waste.aspx/.

[3] http://www.grantadesign.com/products/ces/.