Stack processing

ImageJ is very suitable to process information that has more than two dimensions: data acquired at different Z-levels or at different time points. We have already seen an example of stack processing in the section on noise correction. The next section will deal with time series consisting of frames. However, first, we will explore more options when dealing with image stacks containing slices (Z-stacks).

Processing Z-stacks

Z-stacks are series of 2D images that were acquired at different heights or distances. In a microscope, this is done by moving the objective or the stage up or down and acquiring an image at specific intervals. In Magnetic Resonance Imaging (MRI), this is done by moving the patient through the center of the scanner. The scanner then creates an image for each position using radio pulses that create fluctuations in the magnetic field. These fluctuations can be measured by the detector in an MRI machine. This results in a single slice that can be combined...