The SE detector is located behind and to the left of the conical SEM pole magnet (see image below). Secondary electrons have relatively low energy, and are emitted from the upper several nanometers of the material under the electron beam. The wire cage around the end of the detector is usually set to a positive "bias voltage" of hundereds of volts to collect the secondary electrons even if they exit the sample traveling away from the detector. This makes the SE detector very efficient and able to produce images at very low beam currents. If the bias voltage is set to a modest negative value, low-energy SEs can't reach the detector but higher-energy BSEs can because of their higher energy. This allows the SE detector to act as a BSE detector, though it is not as sensitive as the dedicated BSE detector. It can, however, produce more starkly shadowed images than the BSE detector. Because the detector only measures the number of electrons hitting it, the image result is a gray scale. Images can be colorized later using 3rd party software.

Because SEs come from very close to the sample surface, and because the SE detector is off to the side, it produces shadowed images, giving 3-d effect. For this reason, it is best for imaging the outer surfaces of irregular objects. In setting up the instrument for best imaging there are a couple of things to remember. First, the lower the beam current the better the resolution, all else being equal. Start at 100 pA or so, and a detector bias voltage of +300 V. The highest resolutions can only be attained at the lowest probe currents. Second, adjust beam voltage to suit the sample. High voltages can give better resolution (shorter electron wavelength), but they can also penetrate the surface and provide electrons from deeper in the sample, and even behind the sample, especially for samples with low average atomic number like organic materials. This can be a good or a bad thing, depending on what you are looking for. A classic bad effect is with overlapping organic fibers at too high a beam voltage, where lower fibers can be seen through higher fibers as though they were partially transparent. If you don't like the effect, lower the voltage. An example of a good effect is for thin shells, where some parts are thinner than others (e.g., insect exoskeletons). The variation in thickness at higher voltages results in more secondary electrons coming from thicker parts (brighter). At lower voltages, only the surface shape is imaged.

The secondary electron detector (SE) is to the left of and behind the conical pole magnet.

Polished mineralized fossil. Most striking is the topographic relief evident surrounding flat, polished 'plateaus'. In the plateaus to the right, note that there are two shades of gray, with irregular areas of lighter material in a darker gray matrix. This is caused by an atomic number effect. Generally, the higher the average atomic number, the more SEs and BSEs that reach the SE detector, so the brighter the image. The bright circle to the lower left is a bubble in epoxy. The carbon coat is too thin near the edge and inside the bubble, causing charging which greatly enhances electron yield from the negatively charged surfaces. The same is true for the bright white specks in the middle right and top left.

Fossil spore casing from a coprolite. Bright edges are caused by charging because of too thin a gold-palladium coating. Notice the strong 3-d effect.

Possible insect mandible, from a dissolved coprolite, dispersed on glass.

Impression of a seed on the broken surface of a coprolite.

Spheroids, hollow and filled, that may be fossil bacteria in a coprolite.

Plant fragment separated from a dissolved coprolite, dispersed on glass.