Image Analysis Course for Life Science by Morten Larsen, University of Copenhagen

Ofra Golani's picture

Image Analysis Course for Life Science Faculty.
Material includes: slides, hands-on exercises using ImageJ and related data.
There is a full lecture on ImageJ macro language (session 12).
Website: []

Session 1: The basics: Images - Digital image representation, Image processing and image analysis, Concerns at image acquisition, Pixel-wise transformations, Visual enhancement

Session 2: Filtering and noise reduction - What is filtering? , Noise and noise reduction, Convolution filters, Ranking filters, Anisotropic smoothing, Background subtraction

session 3: Colour (and multispectral) images - Colour and colour spaces, Colour imaging and calibration, Spectral unmixing / Colour deconvolution, Colour thresholding, Principal component analysis

Session 4: Thresholding and binary images - Thresholding, Automatic threshold selection, Binary logic, Masking, Binary morphology, Euclidian distance transform

session 5-6: Object level analysis - From pixels to objects, Counting and characterizing objects, Skeleton and EDT

session 7: The frequency domain - The Fourier transform (1D), The Fourier transform (2D), Interpretation of frequency domain images, Modifications in the frequency domain, Convolution/multiplication duality, The inverse filter and the Wiener filter

session 8-9: Derivatives, edges and texture – Derivatives, Edge detection, The Hough transform, Texture

session 10: Template matching, alignment,interpolation and resampling - Template matching, Correlation in the spatial domain, Image alignment, Correspondance matching, Interpolation, Resampling

session 11: Classification and clustering

session 12: ImageJ macro programming - ImageJ Macros, Image titles and IDs, Invoking macros and installing macro sets, Text output, Generalizing macros

Image Analysis Course for Life Science
Morten Larsen, University of Copenhagen
Average: 5 (1 vote)


bpavie's picture

The link to all slides and document is

czhang's picture

Website link seems not working anymore?