An automated method for evaluating microbial growth on plated media, the method comprising: providing a culture media inoculated with a biological sample disposed in a container that is substantially optically transparent; incubating the inoculated culture media in an incubator; placing the transparent container carrying the inoculated culture media in a digital imaging apparatus; obtaining a first digital image of the inoculated media at a first time (t o), the first digital image having a plurality of pixels; determining coordinates of the pixels in the first digital image relative to the transparent container carrying the inoculated culture media; removing the transparent container carrying the inoculated culture media from the digital imaging apparatus and placing the inoculated culture media in the incubator for further incubation; after further incubation, placing the transparent container carrying the inoculated culture media in the digital imaging apparatus; obtaining a second digital image of the inoculated media at a second time (t x), the second digital image having a plurality of pixels; aligning the first digital image with the second digital image, such that the coordinates of a pixel in the second digital image correspond to the coordinates of a corresponding pixel in the first digital image; comparing the pixels of the second digital image with corresponding pixels of the first digital image; identifying pixels that changed between the first digital image and the second digital image, wherein the pixels that have not changed between the first digital image and the second digital image are indicative of background; determining which of the identified pixels in the second digital image have a predetermined level of threshold contrast with the pixels indicative of background; identifying one or more objects in the second digital image, each object consisting of pixels that meet said level of threshold contrast and that are not separated from each other by background pixels; for at least one of the identified objects, determining a morphology of the object from the pixels of the object by obtaining object features from the pixel information associated with the object, wherein the object features comprise at least one of object shape, object size, object edge and object color, wherein the morphology of the object is determined based on the object features; and from the morphology of the object, determining whether the object is a colony candidate; and providing to memory the coordinates of the pixels associated with the object. providing a culture media inoculated with a biological sample disposed in a container that is substantially optically transparent; incubating the inoculated culture media in an incubator; placing the transparent container carrying the inoculated culture media in a digital imaging apparatus; obtaining a first digital image of the inoculated media at a first time (t o), the first digital image having a plurality of pixels; determining coordinates of the pixels in the first digital image relative to the transparent container carrying the inoculated culture media; removing the transparent container carrying the inoculated culture media from the digital imaging apparatus and placing the inoculated culture media in the incubator for further incubation; after further incubation, placing the transparent container carrying the inoculated culture media in the digital imaging apparatus; obtaining a second digital image of the inoculated media at a second time (t x), the second digital image having a plurality of pixels; aligning the first digital image with the second digital image, such that the coordinates of a pixel in the second digital image correspond to the coordinates of a corresponding pixel in the first digital image; comparing the pixels of the second digital image with corresponding pixels of the first digital image; identifying pixels that changed between the first digital image and the second digital image, wherein the pixels that have not changed between the first digital image and the second digital image are indicative of background; determining which of the identified pixels in the second digital image have a predetermined level of threshold contrast with the pixels indicative of background; identifying one or more objects in the second digital image, each object consisting of pixels that meet said level of threshold contrast and that are not separated from each other by background pixels; for at least one of the identified objects, determining a morphology of the object from the pixels of the object by obtaining object features from the pixel information associated with the object, wherein the object features comprise at least one of object shape, object size, object edge and object color, wherein the morphology of the object is determined based on the object features; and from the morphology of the object, determining whether the object is a colony candidate; and providing to memory the coordinates of the pixels associated with the object.