using-process-batch.md

Using [ Process > Batch ]

This documents contains few examples on how to use [ Process > Batch ]

Activity: Paint filenames into images

It is good practice to have meaningful filenames, e.g., containing a particular treatment that your images were subjected to. For quick visual inspection of your data it can thus be useful to display the filename in the image.

Workflow:

• Use ImageJ's in-built batch processing, chosing one of the example macros.
  • [Process > Batch > Macro]
    • Input: "../data/meaningful-filenames/"
    • Output: your choice
    • Combine code from two of the example macros: "Print index and title", "Label"
      • setFont("SansSerif", 18, "antialiased");
      • setColor("red");
      • drawString(getTitle(), 20, 30);
    • [Process]

Don't worry for now too much about the code; we will learn more about it later.

Activity: Macro recording for putting a scale bar on multiple images

It is also very useful to have a scale bar in the images, e.g. for publication on a web-site. There is no predefined macro for adding a scale bar in Process > Batch; thus we have to record the command on our own.

Workflow:

• Record the macro command for putting a scale bar:

  • [Plugins > Macros > Record..]
    • Record: Macro (not Java)
  • Open some file, e.g. "../data/meaningful_filenames/Treatment_A.tif"
  • Put a scale bar:
    • [Analyze > Tools > Scale Bar..]
      • choose some parameters that you like
      • [OK]
  • Now the window should show some text, such as:
    • run("Scale Bar...", "width=50 height=4 font=14 color=White background=None location=[Lower Right] bold");

• Use the recorded text (copy & paste) to put a scale bar onto multiple images using [Process > Batch > Macro..] (see above)