Method and system of developing an imaging configuration to optimize performance of a microscopy system

A system for operating a microscopy system, comprising:

• an imaging configuration optimizer operating on one or more processors that receives a first image of a sample acquired using a first imaging configuration;
• a degraded image generator operating on the one of more processors that develops a degraded second image from the first image, wherein the degraded second image simulates an image of the sample that would be acquired if the microscopy system were operated using a second imaging configuration, and wherein the second imaging configuration is a candidate production imaging configuration;
• an image analyzer operating on the one or more processors that applies a sequence of image processing steps to the first image and the second degraded image to develop a first classification, wherein the first classification is associated with first objects represented in the first image;
• and
• an imaging configuration scorer operating on the one or more processors that applies the sequence of image processing steps to the second degraded image to develop a second classification that is associated with second objects represented in the second degraded image, and develops a score associated with the second imaging configuration that represents a difference between the first classification and the second classification;
• wherein the image acquisition time or component requirements of operating the microscopy system is less when operated using the second imaging configuration than when operated using the first imaging configuration.