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Copenhagen Image Analysis 2021
Provider: Faculty of Health and Medical Sciences

Activity no.: 3478-21-00-00There are no available seats 
Enrollment deadline: 27/08/2021
Date and time24.09.2021, at: 09:00 - 01.10.2021, at: 16:30
Regular seats20
Course fee6,600.00 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: fak-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 combPhine 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 (September 24 - introduction to image formation, basics on Fiji and preparation of own projects) followed by 5 days teaching (September 24-October 1). 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, Associate Professor, University of Copenhagen, cprats@sund.ku.dk


Teachers
Chong Zhang, PhD (Universitat Pompeu Fabra, Barcelona, Spain) and S├ębastien Tosi (Institute for Research in Biomedicine, Barcelona, Spain).


Dates
Friday, September 24 and Monday, September 27 to Friday, October 1, 2021


Course location
University of Copenhagen, Panum Institute


Registration
Please register before August 27 2021

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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