The aim of the course is to introduce the use of 3D confocal and light sheet imaging to answer basic and pre-clinical research questions in a quantitative manner, and teach tools for quantitative imaging analysis.

The course includes lectures, inspirational talks and demo workshops in microscopy and image analysis.

The format includes 4 days on-campus teaching and workshops and a post-course assignment and online presentation seminar.

You are expected to read provided material, complete an image analysis tutorial and prepare a 2-5 minute project presentation in preparation for the course.

During the 4 days on-campus course you will be introduced to different 3D bioimaging modalities and learn how to choose the right instrument and analysis methods for your research question. Inspirational talks by leading scientists in exploratory biomedical research, medical imaging, corporate preclinical development, and AI based image analysis will illustrate different implementations of 3D imaging and analysis.

During the course you will have a choice between two microscopy demo workshops with some possibility for hands-on operation: Light sheet microscopy (Miltenyi’s UltraMicroscope Blaze) or confocal microscopy (Olympus’ FV1200).

During the data analysis workshop we will introduce the open-source image analysis software ImageJ/Fiji and the commercial software Imaris, and assist you with setting up your own analysis pipeline in small groups. You will learn how to preprocess, render, and segment images. If you are already in the possession of 3D imaging data you will be able to get started on analysing own data. If you do not have any data, you will be provided with image data. Within one week after the course, you will need to submit a written report presenting the analysis pipeline and results. The course will conclude with oral presentations in an online session.