Analyzing superresolution images with ImageJ

Here we provide few examples of how ImageJ can be used for analyzing super-resolution images.

• Drawing a scale bar
• Measuring size of objects
• Measuring an intensity profile

Drawing a scale bar

1. A scale bar can be drawn using command: Analyze → Tools → Scale Bar ....

Measuring size of objects

1. Draw a region, e.g., free hand selection, around object of interest.
2. Measure the object size using command: Analyze → Measure (Ctrl+M).

Measuring an intensity profile

1. Line selection: set line width (double click on the line tool) and draw a line across the object of interest.
2. Rectangular selection: A rectangular selection can be used only for horizontal intensity profiles. Therefore, the image might need to be rotated first so that the structure of interest is vertical using command: Image → Transform → Rotate ...
3. The intensity profile can be plotted using the command Analyze → Plot Profile (Ctrl+K).