A method for mapping fluid objects (120, 220) on a substrate (110, 310) using a microscope inspection system comprising: providing a microscope inspection system comprising a microscope system and a computer analysis system, wherein the microscope system includes a light source, imaging device, stage for moving a substrate disposed on the stage, and a control module, and wherein the computer analysis system includes an object identification module; and performing a scan of the substrate using the microscope inspection system, the substrate comprising objects; identifying for each object on the substrate, an object position on the substrate including a set of X, Y, and θ coordinates using algorithms, networks, machines and systems including artificial intelligence and image processing algorithms, wherein the X, Y coordinates refer to a coordinate position of an object and the θ coordinate refers to an orientation of the object with respect to a reference point on the object, generating object mapping information that reflects the object position of each of the objects and a shift or deformity amount for each of the objects, wherein generating the object mapping information is done automatically using the algorithms, the networks, the machines and the systems including the artificial intelligence and the image processing algorithms predicting, by an object layout prediction module, future object mapping information for a particular stage of a manufacturing and/or examining process based on the object mapping information, the future object mapping information comprising future X, Y, θ coordinates of the objects and a future deformity of each object; identifying for each object on the substrate at the downstream stage of manufacturing, a second object position on the substrate including a second set of X, Y, and θ coordinates; generating second object mapping information that reflects the second object position of each of the objects and a second deformity amount for each of the object; comparing the second object mapping information to the future object mapping information to determine whether the second object mapping information exceeds a predefined tolerance; if the second object mapping information exceeds the predefined tolerance, generating an alert; and if the second object mapping information does not exceed the predefined tolerance, causing (630A, 630B) the stage, the imaging device, and the objects to be aligned. providing a microscope inspection system comprising a microscope system and a computer analysis system, wherein the microscope system includes a light source, imaging device, stage for moving a substrate disposed on the stage, and a control module, and wherein the computer analysis system includes an object identification module; and wherein the microscope system includes a light source, imaging device, stage for moving a substrate disposed on the stage, and a control module, and wherein the computer analysis system includes an object identification module; and performing a scan of the substrate using the microscope inspection system, the substrate comprising objects; identifying for each object on the substrate, an object position on the substrate including a set of X, Y, and θ coordinates using algorithms, networks, machines and systems including artificial intelligence and image processing algorithms, wherein the X, Y coordinates refer to a coordinate position of an object and the θ coordinate refers to an orientation of the object with respect to a reference point on the object, generating object mapping information that reflects the object position of each of the objects and a shift or deformity amount for each of the objects, wherein generating the object mapping information is done automatically using the algorithms, the networks, the machines and the systems including the artificial intelligence and the image processing algorithms predicting, by an object layout prediction module, future object mapping information for a particular stage of a manufacturing and/or examining process based on the object mapping information, the future object mapping information comprising future X, Y, θ coordinates of the objects and a future deformity of each object; identifying for each object on the substrate at the downstream stage of manufacturing, a second object position on the substrate including a second set of X, Y, and θ coordinates; generating second object mapping information that reflects the second object position of each of the objects and a second deformity amount for each of the object; comparing the second object mapping information to the future object mapping information to determine whether the second object mapping information exceeds a predefined tolerance; if the second object mapping information exceeds the predefined tolerance, generating an alert; and if the second object mapping information does not exceed the predefined tolerance, causing (630A, 630B) the stage, the imaging device, and the objects to be aligned.