Engineer position on development of a virtual platform for device implantation in left atrial appendages
Engineer position on development of a virtual platform for device implantation in left atrial appendages
An engineering position is available at the BCN-MedTech Research Unit (https://www.upf.edu/web/bcn-medtech/), Department of Information & Communication Technologies (DTIC) of the Universitat Pompeu Fabra (UPF), Barcelona, Spain, as part of the EU Horizon 2020 SimCardioTest project (2021-2024; SC1-DTH-06-2020, Grant agreement No. 101016496), ideally starting May 2021.
SimCardioTest is a recently granted European project involving a large consortium of clinical, industrial and academic partners (see Figure 1), with the main goal of developing a standardised and secure cloud-based platform where in-silico trials run seamlessly. UPF is the leader of the cardiac use case related to left atrial appendage occluder (LAAO) devices, where we will demonstrate the platform effectiveness, along with the required verification and validation processes and certification support to optimise LAAO device settings.
Fig. 1. SimCardioTest in-silico trials: a life buoy for healthcare innovation in cardiovascular disease.
LAAO devices are good examples of the most advanced generation of implantable devices that are having a large impact in the treatment of cardiac patients, in particular the ones suffering from atrial fibrillation. Non-valvular atrial fibrillation, the most common sustained cardiac rhythm disturbance in Europe, disrupts the normal behaviour of the heart and creates the appropriate environment to generate thrombus. Around 99% of AF-related strokes originate from thrombus formed in a cavity of the left atrium, the left atrial appendage (LAA).
However, there are still important questions on the selection of the right LAAO device for a given patient as well as the optimal positioning. Clinicians need to select the type and size of the LAAO device to implant, as well as the location to be deployed. Usually, interventional cardiologists make these decisions after the analysis of patient-specific medical images in 2D flat monitors with Multiplanar Reconstruction visualisation, before and during the procedure, and obtaining manual measurements characterising the cardiac anatomy of the patient to avoid adverse events after the implantation. At UPF, we have developed over the last few years the Virtual Implantation and Device selection in left Atrial Appendages (VIDAA) platform (see Fig. 2), which provides a clinician-friendly web-based tool to support the pre-operative planning of LAAO interventions (e.g., Aguado et al., 2019, https://doi.org/10.3389/fphys.2019.00237; see a preliminary beta version here: https://github.com/bcnmedtech/VIDAA). It allows clinicians to interactively explore the LA geometry as a 3D mesh with different Computer-Aided Design LAAO models together with some morphological indices and the original CT images in MPR format. We also developed VRIDAA, the Virtual Reality (VR) version of VIDAA (Medina et al., 2020, https://diglib.eg.org/handle/10.2312/vcbm20201168), for the visualization and analysis of LAA anatomies and the most appropriate occlusion devices to be implanted, which was positively evaluated by clinical users as a source for motivation for trainees and to better understand the required surgical approach before the intervention.
Fig. 2. VIDAA platform developed at UPF for pre-interventional planning of LAAO implantation.
The main goal of this position is to continue the development of VIDAA and VRIDAA to add advanced functionalities such as realistic device deployment, connection of the web-based interface to cloud-based processing of the data, or visualisation of fluid simulation results, among others. Moreover, the candidate will be responsible for processing cases from the clinical collaborators that are helping to design VIDAA and VRIDAA, e.g., physicians and researchers from Hospital Clínic de Barcelona (Barcelona, Spain), Hospital de la Santa Creu I Sant Pau (Barcelona, Spain), Hospital Puerta del Mar (Cádiz, Spain), and Righospitalet (Copenhagen, Denmark). Additionally, VIDAA and VRIDAA will be tested in clinical environments to study their potential fit in current healthcare workflows and translation into daily clinical routine, in comparison with other visualisation techniques such as 3D printing. Adaptation of VIDAA and VRIDAA to other interventional cardiology applications will also be investigated. Within the SimCardioTest project, VIDAA will need to communicate with the in-silico clinical trial platform to be developed.
The current version of the VIDAA platform is based on the Rocket (https://www.upf.edu/web/bia/rocket) and ReImagine frameworks (https://www.upf.edu/web/bcn-medtech/online-processing), developed at UPF over the past few years, which has enabled the creating of several interfaces and applications for different clinical use cases, including advanced processing of data from developing countries (sponsored by the Bill & Melinda Gates foundation and the WHO), and multi-centric lung and cardiac image analysis currently used by several international partners, among others. The candidate working on VIDAA/VRIDAA will need to synchronize her/his work with other software engineers responsible for different use cases.
Universitat Pompeu Fabra was established in 1990 as a public university with a strong dedication to excellence in research and teaching. UPF is the first Spanish university in the world Top 200, positioned in 152nd worldwide and 65th in Europe (Times Higher Education ranking THE2021), and ranked as 10th university under 50 years of age (THE2020) and 5th among young universities in Europe, out of 414 listed institutions. The Department of Information and Communication Technologies (DTIC) of UPF initiated its activity in 1999 and has an important track record of active participation in EU projects (67 H2020 projects with a total budget for the department of 30 million EUR). It is one of the two Spanish ICT departments that had been awarded the Maria de Maeztu excellence by the Spanish government for the quality and relevance of its pioneering scientific research, and as the top IT research concentration in Spain. The DTIC, which has over 60% of international researchers from 48 different countries, is located on the Poblenou campus, in the heart of the Barcelona [email protected] technology district, which includes high-tech companies, technology centres and public administrations, creating an outstanding area for RTD projects.
BCN MedTech is a research unit at UPF that acts as an interdisciplinary and translational platform in biomedical engineering research. It was created in 2016 to integrate transversal competencies in computational methods, tackle health problems and contribute to the technological improvement of the healthcare industry for safer and more predictive medicine. Since then, the unit has been participating in more than 200 RDI projects, 1.000 publications, 19 patents and 57 PhD theses. Activities focus on biomedical image analysis and processing, data mining, complex systems and signal analyses, tissue and organ modelling, multi-scale simulations and biomedical electronics. BCN MedTech has 60 full-time researchers, including one ICREA and 4 faculty professors. It combines international, national and regional projects with the collaboration of both companies and research centres. In 2020, the unit had 7 European, 6 national and 10 regional competitive funds. In 2020, the research unit has been recognized as a TECNIO centre, a label from the Catalan government that acknowledges the value of the research unit's projects in terms of translation of the technology to the market.
Profile of the candidate
We are looking for a highly motivated engineer with an undergraduate degree (or equivalent) in Computer Science, Biomedical Engineering, Physics, or related disciplines, willing to develop web-based platforms and virtual reality interfaces in biomedical engineering applications. Excellence in programming skills is a must, in particular in front-end and web-based technologies (e.g., HTML5; ideally also ReactJS). Basic knowledge in Python is desired; being familiar with Docker, mongoDB and git would also be very positive. Knowledge in back-end framework would be a plus, as well as experience in computer graphics, image processing and data science.
Candidates must have excellent teamwork and communication skills and be enthusiastic about collaborating with a diverse range of partners. We expect them to be fluent in English, as it will be the language used to interrelate with the different partners. Interest in clinical translation is essential since meetings with clinicians will regularly take place. Female applicants are explicitly encouraged to apply and will be treated preferentially whenever they are equally qualified as other male candidates.
BCN-MedTech offers an ideal working environment, mainly due to the large critical mass of experienced senior investigators in diverse areas of biomedical engineering, junior postdoctoral researchers and an international team of talented young PhD students; there is always someone that can help! In addition, the extensive network of collaborations, including clinical and large infrastructure partners, gives us a privileged access to unique data, software and technological facilities. Moreover, the candidate will closely work with a team of 4-5 software engineers currently developing applications in the Rocket and ReImagine frameworks.
This position will be funded with resources based on the SimCardioTest project. A one-year contract will be offered, with the possibility of extension up to three years, depending on performance. The salary will be around 26200 euros annual gross. After this period, there might be possibilities of being involved in further research and innovation projects in BCN MedTech, as well as in the transfer of the developed technology to other companies or UPF spin-offs.
The selection committee uses a number of indicators to evaluate the applicant’s preparedness, motivation and potential.
1st phase, remote pre-selection:
The Scientific and Technological excellence will be considered at first, based on:
· Quality of the CV, in general
· Any demonstrated experience, particularly if supported by evidence
· Undergraduate performance: with a special focus on relevant field-specific courses
· Any demonstrated previous recognitions (grants, awards, …)
· Reference letters: Two refence letters are expected. Referees are asked to address analytical capabilities, technical proficiency, ability to work independently and motivation/commitment.
· Statement of purpose: past experience, motivation for applying to this particular position, background fit, contribution of the position to the candidate’s future careers plans, ...
· Additional relevant skills (field-specific): demonstrated, e.g., through previous projects, and or through previous participation in contests, trainings, ...
2nd phase, interview(s):
Should the candidate be preselected at phase 1, a second phase will consist in at least one interview through which the motivation, the proactive behaviour, the capacity to work collaboratively, the organizational skills, the communication skills and the capacity to engage in a discussion and manage problems, will be assessed, among other aspects. The final decision will be the result of a consensus of an evaluation committee that will take into account the results of both recruitment phases 1 and 2. The candidate will be informed of the section results by email.
All the documents that prove the eligibility of the candidate and should be provided. As for the selection process candidates are expected to provide at least the following documents:
· A brief introduction letter (no more than one A4 page) that summarizes the documents and the nature of the information provided for the selection
· A full CV
· The two requested reference letters
· The letter of purpose (no more than two A4 pages)
All documents must be sent by email to Pr Oscar Camara <[email protected]>.
Deadline: open until filled.