Course Catalogue

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This course gives students the opportunity to work as an interdisciplinary team to use an automated microscope to solve a challenge typical of a life sciences application. It will require programming, hardware, and experiment design skills, as well as developing teamwork and communication.

There will be an introductory lecture, four two-hour seminars, and 10 x 3 hours practical sessions.

An introductory programming course in Python is required, this is provided on the programme in the first semester, at University College Dublin.

None

The project will be carried out in groups of around 4. Each group will present their solution orally towards the end of the project period in a group presentation worth 25%, and each student will produce a written report worth 25%. Each group will also maintain a shared lab notebook documenting individual contributions, which will be assessed summatively twice during the project and give each student 25% of their grade. The remaining 25% will be based on observations in the lab by the supervising academic and demonstrators. Marks for lab notebook contributions and lab observations will be individual, as will the reports. Presentations will be marked as a group.

This course is designed to improve collaborative and teamwork skills by involving students in a multidisciplinary group project. The project will bring together students from both tracks (PS and LS) and will focus on the implementation of smart microscopy. Furthermore, it aims to develop practical expertise in constructing and operating an OpenFlexure Microscope, encompassing tasks such as equipment installation and dismantling. The course aims to offer practical experience in addressing pertinent imaging issues within a multidisciplinary team, by combining knowledge from diverse scientific domains. Moreover, the objective is to achieve expertise in utilising Python for the purpose of controlling microscopes and acquiring images, specifically for tasks such as capturing tiled scans and performing AI-based image processing tasks. The goal is to comprehend the fundamental principles and methodologies used to synchronise a microscope with external sources of light and/or detectors for the purpose of advanced imaging applications. This course will provide students with hands-on experience, practical skills development, and opportunities for interdisciplinary collaboration, preparing them for real-world challenges in smart microscopy and imaging research.

By the end of this course students will be able to:

■ Plan and communicate effectively in an interdisciplinary team, integrating knowledge from different backgrounds.

■ Build and operate a custom microscope, including equipment setup and teardown.

■ Construct meaningfully complex instrument control scripts, performing tasks such as acquiring tiled scans and multi-scale imaging.

■ Apply programming concepts to tasks such as synchronizing a microscope with external illumination and/or detectors for advanced imaging applications.

■ Evaluate the performance of an instrument or experiment against quantitative metrics.