System and method for template-based image analysis

A computer-implemented system for template-based imaging, comprising:

• an image acquisition module that receives a first image of a first slide, a second image of a second slide, and a third image of a third slide, wherein the third image includes a representation of a sample disposed on the third slide;
• a template generation module that develops a template image from the first image and the second image that identifies first pixels in the template image associated with representations in the first and second images of corresponding first and second reference marks disposed on the first and second slides, respectively, wherein coordinates of the first pixels have a predetermined relationship with coordinates of the representation of the sample in the third image;
• and
• an offset calculation module that aligns the first pixels with second pixels associated with a representation in the third image of a third reference mark disposed on the third slide to develop an offset between the template image and the third image;
• and
• an image segmentation module determines coordinates of third pixels in the third image that are associated with the representation of the sample in accordance with the offset.