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 on 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 perception of the field and its applications being generally misunderstood. We aim to increase the public’s awareness of synthetic biology using a previously inaccessible research tool to highlight the importance of imaging in science.

What are the current options?

In Fig. 1 each microscope has several attributes that make it well suited to its specific niche. It is well known that commercial microscopes are able to produce immensely high quality images and will always be indispensable research tools. However, it is also clear 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 alternatives. These microscopes are created to specifically fulfil their one objective: The FoldScope (a disposable 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 is intended as a more general solution, with each user developing its different aspects to suit their current needs. In this respect, it differs greatly from conventional microscopes.

Social Impact

We envisage OpenScope having a significant impact in many different applications:

Education: Bright field microscopes can be found in most secondary schools and some primary schools. Fluorescence microscopes are far beyond the budget of most schools. By introducing synthetic biology to students at an early stage of education, through the use of fluorescence microscopy, it may be possible to address the communication gap between researchers and the general public. At our Outreach Event there was significant interest from teachers to have synthetic biology and the techniques that underpin it implemented in the school curriculum. OpenScope makes a possibility. It also allows for integrated learning across many STEM subjects including computer programming, 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 a handful for the entire department. Usage time 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 time-lapse imaging. OpenScope is compact, allowing it to be placed within fume hoods or incubators. Lastly, OpenScope addresses the need for highly customisable research equipment that can be tailored to specific experiments

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 provide access to techniques previously reserved for privileged laboratories, and represent a low-cost tool that any lab anywhere in the world can modify and make their own

Integrated Design

Integration of Pre-Existing Microscope

Our design incorporates a number for key features that were developed as part of a contemporary project at the University of Cambridge [5]. 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 uses Dr Bowman's design concepts and develops them in the context of a different microscope type. While the PiScope [5] uses the flexure 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 Specifications page.

Open-Source Hardware and Community 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.

As such, OpenScope has the potential to evolve over time and even diversify into different projects. Scientists and enthusiasts alike will be able to tailor both the hardware and software to their specific needs as a whole or independently. 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 [7] (a low-cost computer). The well-developed community of ‘makers’ associated with these components, and their versatility, 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 [8] as well as the RepRap 3D printer [9].

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

A full life cycle analysis was carried out on OpenScope using using the Eco Audit tool on the CES Selector Program [10]. The program allows for the energy (MJ) and carbon emissions (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 the chassis was instead described as being made using 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 assumes 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: It was assumed that all materials that could be recycled were recycled, the rest were disposed of in landfill

Most energy is consumed from the materials used to make the microscope, at approximately 10 times that of the 'use' energy consumption. It is likely that with a commercial microscope the use and material energy would be closer matched due to the commercial microscope having a much longer lifetime. Although it may seem that a lot of material is used on OpenScope for its short lifetime, much of the material used can be recycled or reused directly. The thermoplastic PLA used to make the majority of the microscope chassis can be recycled to be made into many different products. PLA is derived from renewable resources such as corn starch and sugarcane, and is also fully biodegradable. The other main components of the microscope are the printed circuit boards used in the Raspberry Pi and Arduino. These are modular and open-source and so when no longer needed for use in the microscope can be reprogrammed to carry out other tasks in a different product.

There are further ways to increase the sustainability of OpenScope that were not implemented within our project. The RecycleBot is a piece of open source hardware which has the capability to recycle plastic waste and make it into 3D printing filament [11]. The main power consumption for our project was in fact from the 3D printer (not accounted for in the manufacturing process report). In order to improve sustainability in this case there is the possibility of using renewable energies. The first community-scale solar powered printer was developed by White Gator Labs and was based on a Mendel RepRap variant running RAMPS1.3 [12]. This would also allow for printing in developing countries and isolated regions where access to electricity may be limited. To find out more about the development of 3D printing and personal manufacturing download the pdf below.

References

[5] Sharkey, J., Foo, D., Kabla, A., Baumberg, J. and Bowman, R. (2015). A one-piece 3D printed microscope and flexure translation stage. [online] Arxiv.org. [Accessed 18 Sep. 2015].

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

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

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

[9] 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.

[10] Grantadesign.com, (2015). Granta: CES Selector materials selection software. [online] [Accessed 18 Sep. 2015].

[11] Reprap.org, (2015). Recyclebot - RepRapWiki. [online] [Accessed 18 Sep. 2015].

[12] King, D., Babasola, A., Rozario, J. and Pearce, J. (2014). Mobile Open-Source Solar-Powered 3-D Printers for Distributed Manufacturing in Off-Grid Communities.