Introduction to Image Analysis Software (IAS) 2022 June, 1.5 hp

Course number14,2
Max participants12
Application deadline2022-05-01
Course leaderJeremy Adler
DepartmentDepartment of Immunology, Genetics and Pathology
Visiting address Dag Hammarskjölds väg 20
Post addressRudbeck Laboratory, SE-751 85 Uppsala
DatesJune: 2-3, June: 7-9
LocationRita Levi Montalcini room, RudbeckLab
Course length5 days , 0930-1700
Course reportCourse report 
Course plan 



For students who need to make measurements from images.

The aim is to discover the power of image analysis and become proficient in using the Fiji version of ImageJ and Cell Profile – both open source.

The course is highly interactive, learning about image analysis and the specifics of the software by working with images and answering questions.

At the end of the course students will create an image analysis sequence to automatically address a problem relevant to their own work.

No prior experience of image analysis or software is necessary.

Learning outcomes

To understand the potential of image analysis, the language used and appreciate the practical problems.

Students will be able to use standard software to automatically analyze images and understand the importance of acquiring images of the quality required for the analysis.


In addition to focusing on ImageJ and Cell Profiler, the course will touch on other useful software.

Imaris - 3D visualization and measurement

Huygens - image deconvolution

QuPath - huge image sets

Presentation on Elastik

and at the end will work on a project relevant to their research interest by writing an ImageJ macro (sequence of instructions) to automatically process images.


The course is restricted to 12 applicants.

Applications will be assessed 1 month before the start of the course and applicants notified.


To receive the 1.5hp all sessions must be attended.
At the end of the course each student will present their own project to the class; describing the problem and explaining their solutions.


Works sheets, copies of all presentations and test images will be provided at the start of the course

Teaching staff

Jeremy Adler (BioVis)
Anna Klemm (SciLifeLab BioImage Informatics Facility)

More information

Jeremy Adler
BioVis Platform, Uppsala University
Dag Hammarskjölds väg 20,
Rudbeck Lab
751 85 Uppsala

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