Introduction to Image Analysis Software (IAS) September 2021, 1.5 hp
| Course number | 14,2 |
| Year | 2021 |
| Type | Methodcourse |
| Track | - |
| Max participants | 12 |
| Application deadline | 2021-08-08 |
| Language | En |
| Course leader | Jeremy Adler |
| Department | Department of Immunology, Genetics and Pathology |
| Visiting address | Dag Hammarskjölds väg 20 |
| Post address | Rudbeck Laboratory, SE-751 85 Uppsala |
| Dates | 9-14 September |
| Location | Rita Levi Montalcini room, RudbeckLab |
| Course length | 5 days , 0930-1700 |
| Course report | |
| Course plan |
Description
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.
Contents
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
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.
Instructions
The course is restricted to 12 applicants.
Applications will be assessed 1 month before the start of the course and applicants notified.
Examination
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.
Literature
Works sheets, copies of all presentations and test images will be provided at the start of the course
Teaching staff
Lecturer:
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
jeremy.adler@igp.uu.se
070-1679349