The microscope body tube separates the objective and the eyepiece and assures continuous alignment of the optics. It is a standardized length, anthropometrically related to the distance between the height of a bench or tabletop (on which the microscope stands) and the position of the seated observer’s eyes. It is typically fitted with a rotating turret that permits objectives of different powers to be interchanged with the assurance that the image position will be maintained. Traditionally, the length of the body tube has been defined as the distance from the upper end of the objective to the eyepiece end of the tube.

A standard body-tube length of 160 mm (6.3 inches) has been accepted for most uses. (Metallographic microscopes have a 250-mm [10-inch] body tube.) Microscope objectives are designed to minimize aberrations at the specified tube length. Use of other distances will affect the aberration balance for high-magnification objectives. Therefore, focusing of the traditional microscope requires moving the objective, the tube, and the eyepiece as a rigid unit. To achieve this, the entire tube is fitted with a rack-and-pinion mechanism that allows it, together with the objective and the eyepiece, to be moved toward or away from the specimen.
The specimen is usually mounted on a glass slide. Routine microscope slides were fixed at 3 × 1 inches during the Victorian era and are still produced at the metric equivalent of those dimensions (7.5 × 2.5 cm) today. The specimen, usually immersed in a material with an R.I. that matches that of the slide, is covered with a thin cover slip. The mechanical stage on which the slide lies is fitted with a pair of controls featuring a rack-and-pinion arrangement. This permits the glass slide to be moved across the stage in two directions, so that different areas of the specimen can be examined. Computer-controlled microscopes track the position of the slide and can return to designated areas of the specimen when required to do so.
The accuracy with which the focusing and the movement of the slide have to be maintained increases as the depth of focus of the objective decreases. For high-N.A. objectives, this depth of focus can be as small as 1 or 2 μm, which means that the mechanical components must provide stable motion at even smaller increments.
Several approaches have been introduced to achieve such precise stable motion at reasonable cost. Some designers have eliminated the sliding mechanism of the body tube, incorporating adjustments for the vertical movement needed for focusing, as well as the lateral motion of the object, in a single mechanical system. An alternative approach has been to mount a relay objective doublet of 160 mm (6.3 inches) focal length into the lower end of the tube. This tube lens is designed to accept light from an image created by the objective at infinity. The objective itself is designed to have aberrations corrected for an infinite image distance. An advantage of this approach is that, since the relayed image is at infinity, the microscope objective itself, a very lightweight component, can be moved to effect focusing without upsetting the correction of aberrations.
In some microscopes the eyepiece is designed as a portion of a zoom lens, which permits continuous variation of the magnification over a limited range without loss of focus. Such microscopes are widely used in industry.