INSTRUMENT IN-SIGHT: Design Considerations for Optical Systems in Life Science Applications


Research in the life sciences and modern medicine is often, quite literally, about illuminating the unknown. Many analytical techniques and instruments that have been central to advancing the fields of genomics, immunology, oncology, and others, generate light and detect how it interacts with biological molecules and systems.

For that reason, the design and development process for optical systems and assemblies is particularly important to the overall development of a new bioanalytical instrument or medical device. Without the proper considerations, careful planning, and advances in optical technology there would be fewer accessible, user-friendly, next-generation sequencing (NGS), digital droplet PCR (ddPCR), or spatial transcriptomics instruments to advance our understanding of basic biology or diagnose and treat patients.


Navigating the many choices required to take your proof-of-concept optical system to market can be daunting. You’ve gotten your current setup working with off-the-shelf parts and an aligned optical system laid out on one or multiple breadboards and that is an empowering achievement. But commercialization and penetration into a competitive marketplace requires simplification and careful consideration of the needs of your users.

Your optical system may also need to interface with multiple fluidics, hardware, and software subassemblies. Developing all of these in parallel and ensuring that your instrument comes off an assembly line with a perfectly aligned optical system for your customers requires input from several experts and partners in
different disciplines.

Many specialized optics consultants or design firms may require you to set the requirements and specifications without the input of their experts or an inkling of if your current setup can be simplified into a commercially viable product. Selecting the right optical system, how it can best fit into your instrument’s design, and meet the needs of your
customers all require teamwork with the right partner that knows the industry and is engaged beyond a simple transactional service.


Typically, those that embark on the instrument development path have a single goal: make the best instrument for the least amount of money. As you navigate this road, you and your development partners will be faced with many early design choices, which can have a significant downstream impact on the quality and cost of your manufactured product. It’s best to be aware of these and consider them in advance, rather than be caught off guard later in the development process.

Building a Customized Optical System: Designing for “Usability”
When you think about creating a custom optical system, your immediate next thought might be, “How much is that going to cost?” But the confocal or inverted microscope you’ve purchased from Nikon or Olympus for your foundational work may have cost your team hundreds of thousands of dollars. Furthermore, off-the-shelf fluorescent microscopes may be equipped with excitation filters or objective lenses that aren’t applicable to your use cases or, importantly, the applications of your potential customers. They can also be overly complicated to use.

This is where designing a custom microscope (or other optical assemblies) can greatly simplify and miniaturize your instrument. It can also allow you to save on costs by removing components your customers won’t need, increasing “useability” and creating a more compact and stable optical system. Ultimately, the costs of designing a custom
optical piece can be competitive with the original system used in your proof-of-concept work and create something that better interfaces with the other subassemblies in your instrument. As you think about scaling up, even if it’s low volume production, the cost savings will scale too.

Keeping Everything in Place: Designing with Shipping in Mind

The end goal of designing and manufacturing an optical system for life science applications is to have an aligned optical train come off the assembly line and arrive in a customer’s lab in the same condition. For simple or complex optical systems, this relies on having each optical element precisely positioned, mounted, and locked in place. Ignoring the complexities of mounting can create an unreliable instrument that comes out of alignment easily.

The first step in determining your approach to optical alignment is determining which components in your optical system, if any, need to be aligned. If your system is accurate enough with the mechanical tolerances that you’ve defined, then there is no need for doing an alignment in the first place. Often, however, certain components will need to be adjusted. After tweaking, all components are fixed in position, and a one-time alignment is done. In situations where optical systems regularly fall out of alignment, active alignment may be needed.

This approach uses motorized mounts that can offer adjustments of optical elements in precise nanometer steps. Additional detectors are also included so there is feedback. Including active alignment, while necessary for certain systems, significantly increases cost and reduces reliability as the motorized mounts, detectors, and software required for active alignment introduce additional risk of misalignment and component failure. In a perfect world, all-optical components in the system would be fixed, without the need for any active alignment.

There’s a lot of Moving Pieces

In the life sciences, optical systems often interface with electrical, fluidics, and software subassemblies. Designing a fully integrated, user-friendly instrument, that can be reliably manufactured requires regular communication between engineering teams, including mechanical, electrical, optical, hardware, and software engineers. It also requires a shared
agreement on the design goals and instrument or device requirements. Without this integration and teamwork, optical subassemblies can get designed in a vacuum, without considering the cost, performance, and overall design
recommendations of the mechanical or software teams.

To stay on budget and schedule, engineering teams need to communicate early and often about their approach and progress. As development moves forward, teams should continue to meet and make sure that parallel workflows all converge on the same common goal, meeting the desired product and cost requirements. This can have downstream cost-saving benefits, as liabilities and risk can be mitigated early on, prior to transfer to manufacturing. In addition, consistent communication between teams can save on the overall cost by avoiding redesign steps late in the design process.


Gener8 is an integrated, full-service design, development, and manufacturing company with over 20 years of experience serving the life science industry. Our world-class optomechanical and optoelectronic engineers and leaders have helped leading-edge companies, from startups to global corporations, develop consumables and instruments that are changing how scientific discovery, clinical translation, and medicine are done.

To learn more, contact us today!

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