Learning ObjectivesAfter completing this lesson, learners should be able to:
Use for loops to repeat operations multiple times
Running a script for multiple files
In an imaging processing workflow you often apply the same operation to several images, several labels, etc. In order to avoid repeating the same code many times we can use control flow statements such as a
for loop. Loops together with
if clauses represent extremely useful tools when programming.
- Open a script editor.
- Open and run a script that contains several repeated operations and explain that you would like to write this part of code in a more simple way.
- Explain the different elements of a numeric
- The loop header, the loop counter/variable, and body
- The initial and end condition
- How the counter is iterated (e.g.
- Using a print command show how the iterator changes
- Take the starting script and modify it using a
Show activity for:
ImageJ Macro, loop structure
ImageJ Macro, example no loop
ImageJ Macro, example with loop
- Open the binary image xy_8bit_binary__nuclei.tif
- Create a macro (or use a pre-defined one) to erode and find boundary of the binary objects
- Modify the macro so that you can perform an arbitrary number of erosions and find their boundary
ImageJ Macro, Multiple erosion
Download the script script_for_loop_erodeband_noloop.ijm. The goal is to perform a series of binary-erosions and compute the outline of these objects.
- Create a variables
maxErodethat sets the number of erode operations
- Create a
forloop to perform
maxErodeoperations, change the name of the image accordingly
- (Advanced) Create a second
forloop that uses
maxErodeas counter. Vary
maxErodefrom 1 to 50
A solution can be found in script_for_loop_erodeband_withloop.ijm
for loop occurs by iterating over a loop variable defined in a loop header. You use
for loops when you know the number of iterations to execute.
While loop does not have a fixed number of iterations. Typically the header contains a condition that is computed within the body of the loop. TODO.
Recommended follow-up modules: