Aim and content

This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. All other participants must pay the course fee.

Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.

Learning objectives
A student who has met the objectives of the course will be able to:
1. Use open source tools (Fiji, Cell Profiler and others)
2. Do basic Macro programming in Fiji (ImageJ) for automated batch analysis of images
3. Understand the principles of image processing and analysis

Content
We will initially use Fiji to illustrate fundamental image analysis concepts, then expand to introduce other software packages such as cell profiler and Ilastik.
The students will learn what a digital image is, how and when to perform basic image processing tasks and how to combine such tasks to perform advanced image processing and segmentation, automated pixel classification and 2D and 3D measurements.
Furthermore, the students will learn basis Macro programming and how to automate analysis of many images.

Participants
PhD students who use microscopy in their PhD project and are in need to learn image analysis tools to extract the information from image sets, and basic programming to automatise image analysis workflows.

Relevance to graduate programmes
The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH:
– All graduate programmes

Language
English

Form
Students will have to submit an image processing project before the course; summarizing a bioimaging experiment and describing the research question.
The course will consist of a course preparation day (June 14 – introduction to image formation, basics on Fiji and preparation of own projects) followed by 5 days teaching (June 17 -21).
The course program includes work on own project sessions with advice, supervision and support from the teachers (3 at least at all times).

Course director
Clara Prats, Assoc. Prof., University of Copenhagen, cprats@sund.ku.dk

Teachers
Clara Prats, PhD, University of Copenhagen
Richard De Mets, PhD, University of Copenhagen
Sébastien Tosí, PhD, Spain
Tricia Loo, PhD, University of Copenhagen
Julia Katharina Mertesdorf, PhD, University of Copenhagen

Dates
14-21st June 2024

Course location
University of Copenhagen, Panum Institute

Registration
Please register before 12 May 2024

Expected frequency
Once a year in June.

Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules.
Applications from other participants will be considered after the last day of enrolment.

Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

Disclaimer:
DDSA has explicit permission from Arcanic and the owners of the https://phdcourses.dk/ website to display the courses on ddsa.dk.