First Steps In Image Analysis: BioVis basic course 2015
An introduction to the language and potential of image analysis
Course Outline: Hands on teaching using the image analysis software ImageJ and a set of images selected to
demonstrate the topics described below.
Duration - 3.5 hours with one coffee/fika/fruit break.
Students must bring a computer with the FIJI version of imageJ installed (http://fiji.sc/Fiji)
Registration: The course will be run once a month, fee of 300sek for academic and 500sek indistrial, register by
email jeremy.adler@igp.uu.se
Part I (3 h)
Hands on session using ImageJ with images selected to demonstrate the following sequence of topics
- Why image analysis is valuable: human visual system is overwhelmed by the amount of data in images and it is very
hard to objectively assess images
- Why ImageJ: Large user base, free, capable
- Pictures are simply arrays of numbers
- Image types: Byte, integer, floating point & monochrome, RGB, stacks, hyperstacks
- Changing the appearance of images: Contrast stretching, LUTs, saving altered images
- Simple measurements: Setting the scale, length, area
- Measurements from regions of Interest (ROIs): Changing and combining ROIs
- Segmentation/thresholding: Selecting areas from which to make measurements
- Processing using two or more images: Background correction, Z projection, movement
- Counting objects
Part II (30 min)
Description of other features of ImageJ and a brief discussion of the advantages of additional image
analysis software available at BioVis
- More Complex Measurements: Colocalization, tracking, movement
- Extending ImageJ: Macros, plugins, batch processing
- Other Image analysis software at BioVis: Huygens, Amira, Imaris, Cell Profiler.
Supporting material provided for the course
Glossary of image analysis terms.
Work sheet for the hands on session (Part I)
Memory stick with demonstration images and documents