An assay system includes an optical imager to acquire high resolution images of assay strips (e.g., lateral flow immunochromatographic test strips) and performs image processing to identify individual assay strips and determine results for each assay strip, by quantifies the presence or absence of test signal line(s) and control signal line(s). Assay strips may be in a holder or carrier contained in a specimen container also holding a specimen. The assay system automatically logs all results and data to a database that stores a high resolution image of the original immunochromatographic assay, the values of test line(s) and control line(s), and the test result. A user interface directs an end user through operation.