Extraordinary transmission based axial imaging (EOT-AIM) for cell microscopy is reported. EOT-AIM uses linear arrays of nanoapertures, each of which samples target fluorescence up to a preset axial distance from surface, in combination with wide-field microscopy for acquisition of lateral images. Current design of nanoapertures provides EOT-AIM with axial super-resolution that is as small as 20 nm for a depth range of 500 nm. Experiments were performed for the measurement of the axial distribution of ganglioside in mouse macrophage (RAW264.7) cells using FITC-conjugated cholera toxin subunit B. The results were successfully confirmed with conventional confocal and total internal reflection fluorescence microscopy.