Graduate School of health and Medical Sciences

Copenhagen Image Analysis 2022
Provider: Faculty of Health and Medical Sciences

Activity no.: 3478-22-00-00
	Enrollment deadline: 04/05/2022

Date and time	03.06.2022, at: 09:00 - 17.06.2022, at: 17:00
Regular seats	20
Course fee	6,480.00 kr.
Lecturers	Clara Prats
ECTS credits	5.20

Contact person	Jacqueline van Hall E-mail address: jacq@sund.ku.dk

Enrolment Handling/Course Organiser	PhD administration E-mail address: phdkursus@sund.ku.dk

Aim and content This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD students at graduate schools in the other Nordic countries. 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 Nordic countries. 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 and Ilastik) 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. 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 3rd - introduction to image formation, basics on Fiji and preparation of own projects) followed by 5 days teaching (June 13th-17th). The course program includes work on own project sessions with advice, supervision and support from the teachers (3 at least at all times). Within 1 week after the course, students will need to submit a course report based on the outcome of their own project. Course director Clara Prats, Assoc. Prof., University of Copenhagen, cprats@sund.ku.dk Teachers Richard De Mets, Dr., University of Copenhagen Sébastien Tosí, Dr., Institute for Research in Biomedicine, Barcelona, Spain Dates Friday: 3 June 2022 Monday - Friday: 13 June - 17 June 2022. Course location University of Copenhagen, Panum Institute Registration Please register before 4 May 2022 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.

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