This study presents a novel miniaturized Hadamard transform fluorescence imaging microscope, by combining a conventional fluorescence microscope with Hadamard transform multiplexing encoding using a one-dimensional movable mask to realize spatial resolution and a linear CCD for multichannel detection. The microscope can provide high-resolution automatically-generated 0-255 gray level HT images for morphological analysis and visualization of a single cell, and normalized HT images for cellular quantitative measurements. The microscope's imaging capability was applied to measure the DNA content in human lymphocyte, chicken erythrocyte and eel erythrocyte, and a comparative study was performed. The results show that the calibrated DNA content in a chicken erythrocyte is 2.32 pg when human lymphocyte is used as the standard, and eel erythrocyte may be a potentially reliable and novel standard for determining DNA contents in other species because it has a stable DNA value of 2.06 pg, with a CV of 4.3% when 20 eel erythrocytes are measured. The results also demonstrate that the HT imaging microscope should be valuable in the fields of medicine and cell biology.