Course Information
14,2
1.5 ECTS
2026-10-31
Other Courses
English
10
2026
Introduction to Image Analysis Software (IAS) 2026 November
Course Leader
Ross Smith
Department
Department of Immunology, Genetics and Pathology
Weeks
v45: November 2,3,4 + v46: November 9,10,11,12,13 + v47: November 18
Location
Rita Levi Montalcini room, RudbeckLab
Duration
9 days in total: 13.00--16.30pm
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 creating ImageJ macros.
A brief presentation of other software is also provided - with a short introduction to Huygens deconvolution, IMARIS, QuPath, Napari and Cell Profiler.
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 required
The aim is to discover the power of image analysis and become proficient in using the Fiji version of ImageJ and creating ImageJ macros.
A brief presentation of other software is also provided - with a short introduction to Huygens deconvolution, IMARIS, QuPath, Napari and Cell Profiler.
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 required
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.
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.
Content
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
IMARIS for 3D rendering and animation
Cell Profiler to create pipelines for automated analysis of cells
QuPath to quantify the very large datasets generated by slide scanners
and Napari to make use of python coding environments
Other popular/useful software will be introduced:
Huygens to improve resolution
IMARIS for 3D rendering and animation
Cell Profiler to create pipelines for automated analysis of cells
QuPath to quantify the very large datasets generated by slide scanners
and Napari to make use of python coding environments
Instructions
The course is restricted to 10 applicants.
Applications will be assessed 1 week before the start of the course and applicants notified.
Applications will be assessed 1 week before the start of the course and applicants notified.
Examination
At the end of the course, each group of students will present a project to the class; describing a image analysis problem and demonstrating their solution. They will answer questions to demonstrate their knowledge of the image analysis principles involved. Full attendance is required unless approved by the course leader.
Literature
Works sheets, copies of all presentations and test images will be provided at the start of the course
Teachers
Lecturer:
Ross Smith (BioVis)
Ross Smith (BioVis)
Contact
Ross Smith
BioVis Platform, Uppsala University
Dag Hammarskjölds väg 20,
Rudbeck Lab
SE-751 85 Uppsala, Sweden
ross.smith@igp.uu.se
072 533 2646
BioVis Platform, Uppsala University
Dag Hammarskjölds väg 20,
Rudbeck Lab
SE-751 85 Uppsala, Sweden
ross.smith@igp.uu.se
072 533 2646