We compared hyperspectral infrared raster maps and images for contrast, definition and resolution of the same samples recorded with a confocal microscope coupled with a synchrotron radiation source vs a Focal Plane Array (FPA) detector equipped microscope. Biological samples (hair and skin sections) and astrophysics samples (meteoritic grains) were used. The samples presented are a few microns in size, such as embedded particles, a single unique cell or thin layer. Our results show that the actual spatial resolution and contrast of FPA images were lower than spectral maps from the confocal microscope. The FPA microscope also produced measurements that lacked accuracy: size of sample features and peak intensity were inaccurately estimated. More surprisingly, the intensity of absorption peaks in the FPA images was lower than the intensity measured from the same sample with a confocal microscope. Our measurements underlined the complementarity of FPA and confocal microscopes. FPA can be used to quickly measure the overall composition of a sample and detect the distribution of its components, but may fail measuring the exact chemical composition of the small features and may not detect weak spectral differences between adjacent positions. The averaging effect of aperture-less systems not only affects image resolution but also lowers their spectral accuracy. Confocal microscopes are inherently slower but give a more accurate measurement of the local composition at the diffraction limit.