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After the tissue is removed from the patient, it is processed in one or both of two major ways:

Histologic sections

This involves preparation of stained, thin (less than 5 micrometers, or 0.005 millimeters) slices mounted on a glass slide, under a very thin pane of glass called a coverslip. There are two major techniques for preparation of histologic sections:

Permanent Sections

This technique gives the best quality of specimen for examination, at the expense of time. The fresh specimen is immersed in a fluid called a fixative for several hours (the necessary time dependent on the size of the specimen). The fixative, typically formalin (a 10% solution of formaldehyde gas in buffered water), causes the proteins in the cells to denature and become hard and "fixed." Adequate fixation is probably the most important technical aspect of biopsy processing.

The fixed specimen is then placed in a machine that automatically goes through an elaborate overnight cycle that removes all the water from the specimen and replaces it with paraffin wax. The next morning, a technical professional, called a histologic technician, or "histotech," removes the paraffin-impregnated specimen and "embeds" it in a larger bloc of molten paraffin. This is allowed to solidify by chilling and is set in a cutting machine, called a microtome. The histotech uses the microtome to cut thin sections of the paraffin block containing the biopsy specimen. These delicate sections are floated out on a water bath and picked up on a glass slide.

The the paraffin is dissolved from the tissue on the slide. With a series of solvents, water is restored to the sections, and they are stained in a mixture of dyes. The most common dyes used are hematoxylin a natural product of the heartwood of the logwood tree, Haematoxylon campechianum, which is native to Central America, and eosin, an artifcial aniline dye. The stain combination, casually referred to by pathologists as "H and E" yields pink, orange, and blue sections that make it easier for us to distinguish different parts of cells. Typically, the nucleus of cells stains dark blue, while the cytoplasm stains pink or orange.

Frozen sections

This technique allows one to examine histologic sections within a few minutes of removing the specimen from the patient, but the price paid is that the quality of the sections is not nearly as good as those of the permanent section. Still, a skilled pathologist and a knowledgeable surgeon can work together to use the frozen section's rapid availability to the patient's great benefit.


The specimen is a liquid, or small solid chunks suspended in liquid. This material is smeared on a microscope slide and is either allowed to dry in air or is "fixed" by spraying or immersion in a liquid. The fixed smears are then stained, coverslipped, and examined under the microscope.

Like the frozen section, smear preparations can be examined within a few minutes of the time the biopsy was obtained. This is especially useful in FNA procedures (see above), in which a radiologist is using ultrasound or CT scan to find the area to be biopsied. He or she can make one "pass" with the needle and immediately give the specimen to the pathologist, who can within a few minutes determine if a diagnostic specimen was obtained. The procedure can be terminated at that point, sparing the patient the discomfort and inconvenience of repeated sticks.

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