Fiji Exercises Collection

By the Image Analysis Collaboratory @ Harvard Medical School

This is a collection of exercises for the open-source Fiji software.

The exercises are designed to be used in a classroom setting, but can also be used for self-study. They are divided into sections, each of which covers a different topic and/or a different aspect of Fiji.

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Here is an example illustrating the structure of the exercises:

1.1 - Image inspection

1. open the single_channel.tif image (drag & drop, or File > Open)

2. Image > Duplicate (IJ:28.9) (shift + d)

3. Analyze > Histogram (IJ:30.10) (h)

4. click Live

5. Image > Adjust > Brightness/Contrast (shift + c)

   • play with Maximum, Minimum, Brightness and Contrast sliders and with Auto, Set and Reset

   • observe the histogram window, what is changing, what is not?

   • click Apply

   • what changed?

You can perform each exercise using the provided image(s) (click the image name to download it - note that downloads may not work properly in Safari) or with your own images.

For certain Fiji commands, references to the ImageJ User Guide are included (e.g. IJ:28.9) as a helpful resource for learning more about Fiji’s features and capabilities.

If a command has a keyboard shortcut, it is indicated in parentheses in bold (e.g. shift + d).

Have fun!