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Image Analysis
Provider: Faculty of Health and Medical Sciences

Activity no.: 3478-20-00-00There are no available seats 
Enrollment deadline: 28/07/2020
Date and time28.08.2020, at: 09:00 - 04.09.2020, at: 16:00
Regular seats12
Course fee10,320.00 kr.
LecturersClara Prats
ECTS credits5.20
Contact personJacqueline van Hall    E-mail address: jacq@sund.ku.dk
Enrolment Handling/Course OrganiserPhD 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

We will initially use FijJi 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 student will learn basic Macro programming and how to automate analysis of many images.

PhD students that use microscopy in their PhD project and are in need to learn image analysis tools to extract the information from image data 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


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 (August 28th - introduction to image formation, basics on Fiji and preparation of own projects) followed by 5 days teaching (August 31-September 4th). 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 from their own project.

Course director
Clara Prats, Associate Professor, University of Copenhagen, cprats@sund.ku.dk

Chong Zhang, PhD (Univeristat Pompeu Fabra, Barcelona Spain) and S├ębastien Tosi (Institute for Research in Biomedicins, Barcelona, Spain).
Assistance from Pablo Hernandez Varas, Thomas Braunstein and Clara Prats (University of Copenhagen).

Friday 28th August and Monday 31th Auguat to Friday 4th September, 2020

Course location
University of Copenhagen, Panum Institute

Please register before 28th of July 2020.

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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