An imaging system comprising: a light-detection subsystem that illuminates a sample or a portion of the sample to activate light emitters within the sample, excites light emission from the light emitters, and records, over a period of time, intermediate output images of light emitters within the sample or the portion of the sample; an image-generation subsystem that - processes each one of the intermediate output images to identify and record initially determined positions of the light emitters within the sample or the portion of the sample, and that - iteratively computes computed output images from light-emitter-position models and iteratively fits the computed output light emitter images to overlapping light-emitter images in the intermediate output images in order to disambiguate overlapping light-emitter images in the intermediate output images, and sums the intermediate images in which overlapping light emitter images have been disambiguated, - to produce a composite image that includes indications of the positions of the light emitters within the sample or the portion of the sample; and an image-interpretation subsystem that iteratively fits geometric primitives to the composite image, produced by the image-generation subsystem, at two or more hierarchical processing levels by iteratively selecting a set of geometrical elements for a currently considered hierarchical processing level; recursively fitting geometrical elements from the set of geometrical elements to an intermediate, refined image from a preceding iteration or, in a first iteration, to the composite image produced by the image-generation subsystem to produce one or more candidate refined images; and selecting at least one candidate refined images for processing in a subsequent iteration or, in a final iteration at a second hierarchical level, in order to produce one or more refined and interpreted images of the sample or the portion of the sample. a light-detection subsystem that illuminates a sample or a portion of the sample to activate light emitters within the sample, excites light emission from the light emitters, and records, over a period of time, intermediate output images of light emitters within the sample or the portion of the sample; an image-generation subsystem that - processes each one of the intermediate output images to identify and record initially determined positions of the light emitters within the sample or the portion of the sample, and that - iteratively computes computed output images from light-emitter-position models and iteratively fits the computed output light emitter images to overlapping light-emitter images in the intermediate output images in order to disambiguate overlapping light-emitter images in the intermediate output images, and sums the intermediate images in which overlapping light emitter images have been disambiguated, - to produce a composite image that includes indications of the positions of the light emitters within the sample or the portion of the sample; and - processes each one of the intermediate output images to identify and record initially determined positions of the light emitters within the sample or the portion of the sample, and that - iteratively computes computed output images from light-emitter-position models and iteratively fits the computed output light emitter images to overlapping light-emitter images in the intermediate output images in order to disambiguate overlapping light-emitter images in the intermediate output images, and sums the intermediate images in which overlapping light emitter images have been disambiguated, - to produce a composite image that includes indications of the positions of the light emitters within the sample or the portion of the sample; and an image-interpretation subsystem that iteratively fits geometric primitives to the composite image, produced by the image-generation subsystem, at two or more hierarchical processing levels by iteratively selecting a set of geometrical elements for a currently considered hierarchical processing level; recursively fitting geometrical elements from the set of geometrical elements to an intermediate, refined image from a preceding iteration or, in a first iteration, to the composite image produced by the image-generation subsystem to produce one or more candidate refined images; and selecting at least one candidate refined images for processing in a subsequent iteration or, in a final iteration at a second hierarchical level, in order to produce one or more refined and interpreted images of the sample or the portion of the sample. selecting a set of geometrical elements for a currently considered hierarchical processing level; recursively fitting geometrical elements from the set of geometrical elements to an intermediate, refined image from a preceding iteration or, in a first iteration, to the composite image produced by the image-generation subsystem to produce one or more candidate refined images; and selecting at least one candidate refined images for processing in a subsequent iteration or, in a final iteration at a second hierarchical level, in order to produce one or more refined and interpreted images of the sample or the portion of the sample.