Embedding and Orientation

Bottom of cassette: The bottom of the cassette is the side opposite the cassette lid. This is generally the part of the tissue that will be sectioned first.

Bottom of mold: The bottom of the mold is the side facing down when embedding and will be cut first on the microtome.

Cassette: The cassette is a plastic container used to hold identified specimens. It has two parts: the cassette body and the cassette lid. Both parts have small holes that allow for the fixative and holding solution to associate with the tissue inside the cassette.

Note: We require that all specimens be submitted in cassettes that are labeled using pencil, and that each cassette label be listed on the accompanying requisition form.

Cell blocks: Sometimes collections are a concentration of cells, rather than a piece of tissue. We accept cell aggregate submissions for processing, embedding, and sectioning.

Note: Cell aggregate needs to be wrapped in Histowrap; otherwise, cells will be lost during processing.

Fixation: A fixative alters tissue by stabilizing the protein so that it is resistant to further changes. Ten percent (10%) neutral buffered formalin is considered the universal standard fixative for histology. Tissue should not be stored in fixative for more than two weeks. If immunohistochemical (IHC) staining is required, tissue should not be fixed for more than 72 hours before processing.

Inked margins: Inked tissue helps orient the tissue according to client instruction.

Lumen: The lumen is the central cavity of a tubular or other hollow structure in an organism or cell.

On edge: Embedding any tissue with a wall “on edge” makes all the layers of the tissue's wall microscopically apparent upon cutting (Carson, 2009, p. 431). For example, tissue from colonoscopic, endoscopic, and cervical biopsies, cysts, and gallbladder, and specimens with epithelial layers (e.g., skin) are routinely embedded on edge.

On end: Embedding any tissue with a lumen “on end” makes “all layers of the mucosa, submucosa, and external muscle layers” apparent microscopically upon cutting (Carson, 2009, p. 431). This embedding orientation is routinely applied to tissues with a lumen, such as veins or tissue from the appendix or other bodily tubes.

Top of cassette: The top of the cassette is the side that has the cassette lid.

Top of mold: The top of the mold is the side of the mold holding the cassette during embedding and is closest to the embedder; it is the side opposite of where first cutting will be performed.

Swiss rolls: Colon tissue can be arranged in the shape of a Swiss roll, i.e., the material is rolled around in circles on itself. Embedding colon tissue in the shape of a Swiss roll puts the outer, middle, and inner parts of the colon tissue on edge.


Cutting: Cutting, often referred to as sectioning, is the process of using a microtome to cut sections from an FFPE tissue block. A typical section thickness is 3–5 µm. For contrast, a typical piece of paper is 100 µm thick.

FFPE: Formalin-fixed, paraffin-embedded

Levels: Levels result from the method of gathering sections from multiple transections of a tissue specimen. A section is collected from near the surface of the block, after which a much thicker cross-segment of the block is cut away and discarded (e.g., 50 µm), and then another section is collected. This process can be repeated iteratively until the block has been exhausted of tissue.

Sample: Sample is a synonym for "block," "tissue block,” “FFPE block,” or "specimen.” The term is used when referring to any given tissue piece, whether paraffin embedded or not.

Section: A "section” refers to one full-face slice of an FFPE block from a microtome. Standard practice is to place one section per slide, unless otherwise requested in the “Cutting Instructions” of the ARUP requisition form.

Serial section/ribbon: A string of sections is known as a serial section or tissue ribbon. This is how sections come off the microtome; they are then separated into individual sections and placed on a slide.

Frozen Specimens: Preparation and Embedding

Cryomolds: These molds are used to embed frozen specimens in optimal cutting temperature (OCT) compound. Three different mold sizes are used to accommodate different tissue sizes: standard (25 mm x 20 mm x 5 mm), intermediate (15 mm x 15 mm x 5 mm), and deep (surface size is slightly larger than the standard, and depth is for particularly thick pieces of tissue).

Cryoprocessing: The process of preparing frozen tissue for embedding and cutting is referred to as cryoprocessing. As freezing tissue functions as a physical "fixative," so to speak, the tissue itself does not need to be placed into a chemical fixative. Frozen tissue can be submitted either fresh, wrapped in saline-moistened gauze, on wet ice, or in a 30% sucrose holding solution.

OCT compound: This term stands for "optimal cutting temperature" compound, an admixture of water-soluble glycols and resins used to embed tissue specimens before frozen sectioning on a microtome-cryostat.