E3: Automation with Fiji macros

Preparation

Work with the images in data/fiji/programming/macro3

Questions

1. Open one of the images in Fiji.

2. Open the macro recorder (Plugins > Macros > Record…).

3. Apply a combination of filters and thresholding to segment the objects in the image.

4. When you are satisfied with the result, open the macro editor (Plugins > Macros > Edit…) and copy the relevant lines of code from the recorder window to the editor window.

5. Apply the macro to the other three images. Do you get a good segmentation result? If not, try to improve your macro.

6. Use the following code snippet to process all images in a folder. Save an output mask for each image in the output folder. In the following code, you need to replace the comment // your code for image segmentation goes here with your macro code. Choose an output folder that is different from the input folder, so that the masks do not get mixed up with the input images.

input = getDirectory("Choose Input Directory ");
output = getDirectory("Choose Output Directory ");
list = getFileList(input);
for (i=0; i<list.length; i++) {
    if (endsWith(toLowerCase(list[i]), ".tif")) {
        open(input + list[i]);

        // your code for image segmentation goes here
        // ...

        saveAs("Tiff", output + "mask_" + list[i]);
        run("Close All");
    }
}