The advantages of ATR in microscopy.
Of course, each technique has its pros and cons but especially in FT-IR microscopy, transmission and reflection face similar boundaries that limit their applicability.
In contrast, ATR produces high quality FT-IR data of almost any sample type without prior preparation. Furthermore, it also gives you the edge when it comes to spatial resolution.
The germanium crystal acts as a solid immersion lens, improving spatial resolution by factor 4, when compared to transmission and reflection measurements. This way, you easily analyze samples as small as a few microns.
In transmission, samples must be thin enough for IR radiation to penetrate them. For most samples, this requires time-consuming sample preparation, such as the cutting of delicate microtome sections.
If small fibers or microparticles are to be examined, costly filters and pressure cells must be used that allow IR light to pass freely.
In reflection, samples require either smooth, polished and IR-reflecting surfaces or are placed on an aluminum or gold mirror. In the latter case, the samples must also be very thin to allow enough IR light to pass through to obtain a suitable IR spectrum. In addition, reflection spectra often require special data processing for evaluation.