Output is where the Processor will automatically store output images. Input is the folder where you store the images to be processed. Let us have a look on the settings of the Batch Processor (Fig. 2.8), and demonstrate a simple application example of batch processing for data inspection (see Sect. 2.7.5).įinally, we will explore how to handle collecting data during batch processing (see Sect. 2.7.4), or to run the macro from command line in “headless” mode (see Sect. This allows you to use the “batch” button in the Script Editor (see Sect. Moreover, by using an ImageJ2 functionality called “script parameters” (Rueden et al., 2017), it is possible to further enhance the generality of the scripts (see Sect. In that case you just need to know how to handle file path operations and file naming (see Sect. If you know how to run for-loops with ImageJ macro, to include batch processing might be quite an easy job. Though the GUI-based method is easy to use, the scripting based method of batch processing is more flexible to customize. One weak point of the GUI method is that it does not allow you to customize the saving of images and analysis results. This method is also good when you need to quickly document and provide information how to process many images by batch processing. You just need to acquire macro commands using the Command Recorder, and copy & paste those commands in the GUI (see Sect. The GUI-based method is convenient if you are unsure about your capability in writing macros. Each method is optimized for certain usage, and it is good to know all of them so that you can select a suitable method depending on the situation. They are redundant with their goal, but are different in the way they are designed and used. With Fiji, there are multiple ways to do batch processing and analysis (Schindelin et al., 2012 Schneider et al., 2012).
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