Introduction to Image Analysis Software September 2023, 1.5 hp

Beskrivning

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.

Inlärningsmål

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.

Innehåll

Learn about image analysis with an in depth examination of ImageJ and workflows using ImageJ macros.

Other popular/useful software will be introduced:

Huygens to improve resolution

Cell Profiler to create pipelines for automated analysis of cells

QuPath to quantify the very large datasets generated by slide scanners

Undervisning

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.

Litteratur

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

Lärare

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

Kontakt

Jeremy Adler
BioVis Platform, Uppsala University
Dag Hammarskjölds väg 20,
Rudbeck Lab
751 85 Uppsala
jeremy.adler@igp.uu.se
070-1679349

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