A method of analysing a plurality of biological entities using an imaging apparatus. The method comprises: providing a marker for said plurality of biological entities, said marker being capable of identifying objects within said plurality of biological entities when detected using the imaging apparatus, the method of provision being arranged such that said marker is capable of identifying said objects during a first time period, and said marker is less capable of identifying said objects during a second time period; during the first time period, recording a marked-up image in which spatial definitions of said objects are identifiable from said marker; during the second time period, recording a first image of said plurality of biological entities; and generating a spatial definition for an object in said first image using data derived from said marked-up image.