An imaging data processing apparatus for processing imaging data sets, each processing imaging data set forming a corresponding first image of the sample and comprising a set of data acquired by performing a predetermined analysis or observation in each of a plurality of micro regions within a two-dimensional measurement region on a corresponding sample, wherein the imaging data sets are acquired for each of a plurality of samples in which from observation target sites of the sample, or acquired by different analyses or observation methods or under different parameters for an observation target site of one sample, the imaging data processing apparatus comprising:
- a) an image alignment processing unit configured to obtain image deformation information by performing deformation processing of one or more optical images corresponding to the first images to generate one or more corresponding deformed optical images, so that observation target sites represented in the optical images coincide with each other, and perform deformation processing of the one or more of the first images to generate one or more corresponding second images by using the image deformation information obtained by the optical image corresponding to the first image, each second image providing a shift of a position of one or more of the micro regions with respect to their position in the corresponding first image;
- b) a region of interest setting unit configured to obtain a user input to set a region of interest on a reference image, the reference image comprising one of the first images or one of the second images and to set a region of interest on each of the second images that is not the reference image based on the setting of the region of interest on the reference image;
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- c) a region of interest correspondence determination unit configured to determine which micro regions of the second images are included in the region of interest of each second image by determining if a center point of each micro region of the second image exists within the region of interest of the second image.