PhD-level course in Quantitative Microscopy, 5+1-5 ECTS credits

In collaboration between the Centre for Image Analysis, SciLifeLab and BioVis October-December 2012, Language: English
Course web page:
Schedule and Lecture notes:
Schedule for final project presentations, December 11, 2012:

Different kinds of microscopy are becoming more and more common as tools for research in science and medicine. The resulting digital images contain information in up to five dimensions, including three spatial dimensions, time and spectral signatures. Very often, the analysis of microscopy data is limited to visual inspection, but with knowledge about the information content, quantitative measurements can be extracted from the data, increasing the value of any scientific experiment. The aim of this course is to provide knowledge about different sample preparation and microscopy imaging techniques, and give a wide perspective on what kinds of information that can be extracted from microscopy image data, and how this can be approached using digital image processing. After completing the course, the participants will have a better understanding of the possibilities and limitations of different microscopy imaging techniques and will be able to evaluate sample preparation and imaging techniques based on their unique features. The participants will also understand how image acquisition should be optimized for quantitative analysis and understand the basics of how digital image processing can be used to extract quantitative information. Finally, the participants will, after completed course, understand the workflow from sample preparation to quantitative measurements for a specific research application defined based on their own research interests and realized through a multidisciplinary practical project. The practical projects will be carried out collaboratively between students specialized in digital image processing, and students from the application areas.

Contents, study format and form of examination

The course consists of theoretical lectures describing and comparing different aspects of microscopy systems with focus on the relation between the observed object and the created image. Invited lecturers with expertise and long experience working with microscopy will describe the physical and mathematical principles of the imaging systems and discuss limitations and possibilities. They will also discuss basic aspects of sample preparation and quantification, such as describe the relationship between the imaged signal and the physical properties of the sample. Lecturers from the Centre for Image Analysis will describe the basics of digital image processing with focus on microscopy, including illumination correction, object detection, digital stereology, feature measurements and object classification. Hands-on tutorials on example software will also be provided. The examination of this part of the course (5 ECTS) will consist of a written exam.

Finally, the course includes a practical part where 1-2 students with a background in digital image processing (or similar) will be paired up with 1-2 students from an application area, and they will jointly chose a microscopy system around which they design a quantitative microscopy project. The project should include all steps from sample preparation (where the student from the application area acts as the expert, teaching the others), via microscopy, to digital image processing and quantification (where the participant from digital image processing acts as an expert, teaching the others). The project may very well be in line with the students' current research activities. The examination of this part of the course will be a written report and an oral presentation for all course participants, including a discussion of the choice of microscopy system. The examiner and the students will jointly decide the course credits assigned for the project (1-5 ECTS). The oral presentations are mandatory to attend for all students.

Target group/s and recommended background

Basic knowledge of mathematics, physics and biology are recommended. Any student using microscopy as a research tool will benefit from participating in the course.

Department with main responsibility

The course is organized by the Department of Information Technology, Division of Visual Information and Interaction, Centre for Image Analysis, in collaboration with the BioVis platform of the Science for Life Laboratory. PhD students (and if space allows also MSc students) are invited primarily from the departments with in the faculty where microscopy is used as a research tool. Students from other faculties and universities may also join the course. We see the course as a way to increase the number and depth of interdisciplinary collaborations between different fields of science.

All lecture will be in the seminar room at the Centre for Image Analysis, House 2, Polacksbacken, Uppsala. In order to make the course easier to attend for traveling students, lectures will be held on 6 consecutive Tuesdays, 10-15, starting October 9. Projects will be presented on December 11, and the written exam is scheduled for December 12.

How to apply

The course has already started, but if you are interested in future courses, please send in an application.
1. Name, contact info, affiliation, and brief description of current research and motivation for joining the course (maximum 100 words).
2. List of microscopes available at the local facility and available for the project works (if any), and any specific wishes for testing other microscopy systems.
This information will be used to pair students in the best possible way.
and be sent to Carolina Wählby,
Schedule and Lecture Notes:

PS. For more inspiration, read this recent editorial from Nature Methods on The quest for quantitative microscopy .