To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis.
Poster presentatiion, project Printing Makes Sense at Saxion Research Conference 2018, Deventer. Photonics is declared one of the key enabling technologies by the European Commission. Photonics finds its application in many fields ranging from health & well-being to smart industries. Automation in photonics manufacturing and packaging is key to reduce assembly costs. At the NanoPhysics Interface group, we investigate how to quickly couple light from one fiber to another fiber (or photonic devices). After developing a theoretical model and performing measurements, we find that the alignment is most critical in the lateral translations (x and y-direction) and that pre-alignment of the photonic components can be realized by a smart design of the chip holder
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Photonic biosensors for medical diagnostics have been in development for some time. They have proven to show equal or better performance as compared to other techniques in terms of sensitivity, accuracy, and reliability. In order for companies to successfully introduce these sensor products on the market, they must also perform equal or better in price per test and usability. The price per test is to a large extent determined by the costs of the (disposable) cartridge containing the sensor chip and bioactive layer. If the active components can be left out of the cartridge a significant cost reduction can be obtained. However, this adds the challenge of coupling light from the source to the sensor chip inside the cartridge and back onto detectors. This coupling requires a positioning accuracy in the (sub-) micrometer regime. Here, we present a demonstrator system, which implements an passive alignment step followed by an active alignment procedure. The initial alignment is realized with high accuracy when placing a cartridge in an acceptor slot. This results in finding a “first light” state, which allows the active alignment to take over. Active alignment is then realized by moving the fiber by means of a set of actuators to the position with optimal coupling efficiency. A demonstrator was designed and manufactured to test the influence of several key parameters, such as the influence of production accuracy of the cartridges on the initial alignment. The resulting system has shown to comply with the requirements of ease of alignment along with full automation.
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A-das-PK; een APK-straat voor rijhulpsystemen Uit recent onderzoek en vragen vanuit de autobranche blijkt een duidelijke behoefte naar goed onderhoud, reparatie en borging van de werking van Advanced Driver Assistance Systems (ADAS), vergelijkbaar met de reguliere APK. Een APK voor ADAS bestaat nog niet, maar de branche wil hier wel op te anticiperen en haar clientèle veilig laten rijden met de rijhulpsystemen. In 2022 worden 30 ADAS’s verplicht en zal de werking van deze systemen ook gedurende de levensduur van de auto gegarandeerd moeten worden. Disfunctioneren van ADAS, zowel in false positives als false negatives kan leiden tot gevaarlijke situaties door onverwacht rijgedrag van het voertuig. Zo kan onverwacht remmen door detectie van een niet bestaand object of op basis van verkeersborden op parallelwegen een kettingbotsing veroorzaken. Om te kijken welke gevolgen een APK heeft voor de autobranche wil A-das-PK voor autobedrijven kijken naar de benodigde apparatuur, opleiding en hard- en software voor een goed werkende APK-straat voor ADAS’s, zodat de kansrijke elementen in een vervolgonderzoek uitgewerkt kunnen worden.
Various companies in diagnostic testing struggle with the same “valley of death” challenge. In order to further develop their sensing application, they rely on the technological readiness of easy and reproducible read-out systems. Photonic chips can be very sensitive sensors and can be made application-specific when coated with a properly chosen bio-functionalized layer. Here the challenge lies in the optical coupling of the active components (light source and detector) to the (disposable) photonic sensor chip. For the technology to be commercially viable, the price of the disposable photonic sensor chip should be as low as possible. The coupling of light from the source to the photonic sensor chip and back to the detectors requires a positioning accuracy of less than 1 micrometer, which is a tremendous challenge. In this research proposal, we want to investigate which of the six degrees of freedom (three translational and three rotational) are the most crucial when aligning photonic sensor chips with the external active components. Knowing these degrees of freedom and their respective range we can develop and test an automated alignment tool which can realize photonic sensor chip alignment reproducibly and fully autonomously. The consortium with expertise and contributions in the value chain of photonics interfacing, system and mechanical engineering will investigate a two-step solution. This solution comprises a passive pre-alignment step (a mechanical stop determines the position), followed by an active alignment step (an algorithm moves the source to the optimal position with respect to the chip). The results will be integrated into a demonstrator that performs an automated procedure that aligns a passive photonic chip with a terminal that contains the active components. The demonstrator is successful if adequate optical coupling of the passive photonic chip with the external active components is realized fully automatically, without the need of operator intervention.
Physical rehabilitation programs revolve around the repetitive execution of exercises since it has been proven to lead to better rehabilitation results. Although beginning the motor (re)learning process early is paramount to obtain good recovery outcomes, patients do not normally see/experience any short-term improvement, which has a toll on their motivation. Therefore, patients find it difficult to stay engaged in seemingly mundane exercises, not only in terms of adhering to the rehabilitation program, but also in terms of proper execution of the movements. One way in which this motivation problem has been tackled is to employ games in the rehabilitation process. These games are designed to reward patients for performing the exercises correctly or regularly. The rewards can take many forms, for instance providing an experience that is engaging (fun), one that is aesthetically pleasing (appealing visual and aural feedback), or one that employs gamification elements such as points, badges, or achievements. However, even though some of these serious game systems are designed together with physiotherapists and with the patients’ needs in mind, many of them end up not being used consistently during physical rehabilitation past the first few sessions (i.e. novelty effect). Thus, in this project, we aim to 1) Identify, by means of literature reviews, focus groups, and interviews with the involved stakeholders, why this is happening, 2) Develop a set of guidelines for the successful deployment of serious games for rehabilitation, and 3) Develop an initial implementation process and ideas for potential serious games. In a follow-up application, we intend to build on this knowledge and apply it in the design of a (set of) serious game for rehabilitation to be deployed at one of the partners centers and conduct a longitudinal evaluation to measure the success of the application of the deployment guidelines.
