In studying and interpreting stained tissue sections, it is important to remember that microscopic preparations are the end result of a series of processes that began with collecting the tissue and ended with mounting a coverslip on the slide. Certain steps in this procedure may distort the tissues slightly, producing minor structural abnormalities called artifacts not present in the living tissue.

One such distortion is minor shrinkage of cells or tissue regions produced by the fixative, by the ethanol, or by the heat needed for paraffin embedding. Shrinkage can create artificial spaces between cells and other tissue components. Such spaces can also result from the loss of lipids, glycogen, or low-molecular-weight substances not preserved by the fixative or removed by the dehydrating and clearing fluids. Slight cracks in sections also appear as large spaces in the tissue.

Other artifacts may include small wrinkles in the section (which the novice may confuse with linear structures such as blood capillaries) and precipitates from the stain (which may be confused with cellular structures such as cytoplasmic granules). Students must be aware of the existence of artifacts and able to recognize them.

Another difficulty in the study of histologic sections is the impossibility of differentially staining all tissue components on one slide. A single stain can seldom demonstrate well nuclei, mitochondria, lysosomes, basement membranes, elastic fibers, etc. With the light microscope, it is necessary examine preparations stained by different methods before an idea of the whole composition and structure of a cells with all its internal structure of a cell or tissue can be obtained. The TEM allows the observation of cells with all its internal structures and surrounding ECM components, but only a few cells in a tissue can be conveniently studied in these very small samples.

Finally, when a structure's three-dimensional volume is cut into very thin sections, the sections appear microscopically to have only two dimensions: length and width. When examine a section under the microscope, the viewer must always keep in mind that components are missing in front of and behind what is being seen because many tissue structures are thicker than the section. Round structures seen microscopically may be portions of spheres or tubes. Because structures in a tissue have different orientations, their two-dimensional (2D) appearance will also vary depending on the plane of section.

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