Slide 4 of 27
The X-ray diffraction experiment fits into the middle of this sequence (which extends beyond the top left to the protein (or other molecule) and the organism, and beyond the bottom right to building, refinement, interpretation, etc. Integration and scaling are the part of the X-ray experiment which turn the raw data from the images into a more useful form for the subsequent steps.
Mosflm integrates the images and writes the Lorentz and polarization corrected intensities to a multi-record MTZ file.
Each image in a dataset probably has its recorded intensities on a different scale for a variety of reasons, e.g. variation in intensity of the incident radiation, absorption of diffracted rays, change in the diffracting volume, etc. In the process of merging symmetry equivalent reflections from different images, we need to take this into account and apply scales accordingly. This process is performed by SCALA.