An imaging system comprising: a light-detection subsystem - for illuminating a sample or a portion of the sample to excite light emission from light emitters within the sample, and - for recording, over a period of time, the light emission from the light emitters as image data comprising light-emitter images of light emitters within the sample or the portion of the sample; and an image-generation subsystem: - for processing the recorded image data to identify and record positions of the light emitters within the sample or the portion of the sample to generate an intermediate image, the processing step comprising: disambiguating overlapping light-emitter images in the image data, wherein the overlapping light-emitter images are formed by light emission of light-emitters separated from one another by less than a diffraction-limiting distance of the light-detection subsystem, and wherein overlapping light-emitter images are disambiguated by: (i) identifying initial light emitter positions in overlapping light-emitter images; and (ii) iteratively computing, starting from the initial light emitter positions, computed light emitter output images from light-emitter-position models and fitting the computed output light emitter images to overlapping light-emitter images in the image data, and - for producing, from a plurality of intermediate images, a composite image that includes indications of the positions of the light emitters within the sample or the portion of the sample. a light-detection subsystem - for illuminating a sample or a portion of the sample to excite light emission from light emitters within the sample, and - for recording, over a period of time, the light emission from the light emitters as image data comprising light-emitter images of light emitters within the sample or the portion of the sample; and - for illuminating a sample or a portion of the sample to excite light emission from light emitters within the sample, and - for recording, over a period of time, the light emission from the light emitters as image data comprising light-emitter images of light emitters within the sample or the portion of the sample; an image-generation subsystem: - for processing the recorded image data to identify and record positions of the light emitters within the sample or the portion of the sample to generate an intermediate image, the processing step comprising: disambiguating overlapping light-emitter images in the image data, wherein the overlapping light-emitter images are formed by light emission of light-emitters separated from one another by less than a diffraction-limiting distance of the light-detection subsystem, and wherein overlapping light-emitter images are disambiguated by: (i) identifying initial light emitter positions in overlapping light-emitter images; and (ii) iteratively computing, starting from the initial light emitter positions, computed light emitter output images from light-emitter-position models and fitting the computed output light emitter images to overlapping light-emitter images in the image data, and - for producing, from a plurality of intermediate images, a composite image that includes indications of the positions of the light emitters within the sample or the portion of the sample. - for processing the recorded image data to identify and record positions of the light emitters within the sample or the portion of the sample to generate an intermediate image, the processing step comprising: disambiguating overlapping light-emitter images in the image data, wherein the overlapping light-emitter images are formed by light emission of light-emitters separated from one another by less than a diffraction-limiting distance of the light-detection subsystem, and wherein overlapping light-emitter images are disambiguated by: (i) identifying initial light emitter positions in overlapping light-emitter images; and (ii) iteratively computing, starting from the initial light emitter positions, computed light emitter output images from light-emitter-position models and fitting the computed output light emitter images to overlapping light-emitter images in the image data, and (i) identifying initial light emitter positions in overlapping light-emitter images; and (ii) iteratively computing, starting from the initial light emitter positions, computed light emitter output images from light-emitter-position models and fitting the computed output light emitter images to overlapping light-emitter images in the image data, and - for producing, from a plurality of intermediate images, a composite image that includes indications of the positions of the light emitters within the sample or the portion of the sample.