Method and imaging system for matching images of discrete entities

An imaging device for matching a three-dimensional first image of at least one discrete entity with at least a three-dimensional second image of the at least one discrete entity, the discrete entity comprising a biological sample and a plurality of constituent parts of a marker, and the three-dimensional images are acquired by a microscope, the device comprising:

• an imaging container to contain the at least one discrete entity;
• a detector and optical means for imaging at least partially the at least one discrete entity onto the detector;
• and
• a control unit configured to:
• acquire the three-dimensional first image of the at least one discrete entity;
• generate a first representation of the marker from the three-dimensional first image;
• acquire the three-dimensional second image of the at least one discrete entity;
• generate a second representation of the marker from the three-dimensional second image;
• and
• match the three-dimensional first image with the three-dimensional second image by comparing the first representation and the second representation to recognize the at least one discrete entity in subsequent images acquired after the first image,
• wherein generating the first representation and the second representation comprises determining vectors from a position of at least one reference item in the respective three-dimensional image to at least a position of some of the plurality of constituent parts of the marker in the respective three-dimensional image, determining for the vectors at least one value of a property of the vectors, and generating the representation of the marker based on a frequency of the at least one value of the property, wherein the marker is an optically detectable structure, and wherein the at least one reference item is a center of mass of one of the constituent parts of the marker.