Exercise 1 Slides

• Matlab (General Processing, Image Processing Toolbox) [http://www.mathworks.com]
• FIJI (ImageJ with all the plugins already installed): Visualization, Preprocessing, Segmentation, Morphometrics [http://www.fiji.sc]

Once you have logged in

Open a terminal (Accessories -> Terminal)

Type in the following commands exactly!

This will start Fiji

cd /scratch
curl -o qbi.zip http://people.ee.ethz.ch/~maderk/qbi.zip
unzip qbi.zip
cd qbi/
Fiji.app/ImageJ-linux64

Watch this video to see how to open data and visualize it in Fiji http://people.ee.ethz.ch/~maderk/videos/StartingAndVisualizing.swf

The data are in a folder called data inside the qbi folder you just created

• Open with: Fiji/File -> Open …
  • pivo5,6,7raw.tif : A beer foam measured using propagation-based phase contrast at – different times
  • cortical-056_A/B.tif a section of cortical bone taken from a mouse

• Make a new terminal (Accessories -> Terminal)
• Start matlab by typing matlab
• Change to the image directory by typing
  cd /scratch/qbi/data/

• Matlab was designed to process matrices and arrays and consequently treats images as matrices
• Matlab has several built in functions for handling images but offers many more in the Image Processing Toolbox (images).
• You can get an overview of the functions available using the follwing command
  help images
• You can load the image of cortical bone into a variable called cort_img by using the imread command cort_img=imread('cortical-056_A.tif');

• You can show the image using the imagesc command
  imagesc(cort_img);
• You can create a histogram for the image using the hist command
  hist(double(cort_img(:));

• Load the cell image and show it cellImage=imread('http://imagej.nih.gov/ij/images/Cell_Colony.jpg'); cellImage=double(cellImage); imagesc(cellImage);

• Situationally dependent performance
  Are the bands uniform in brightness?

• Situationally dependent performance
  Are the bands uniform in brightness?