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The page below is a sample from the LabCE course Basic Tissue Orientation and Paraffin Embedding Technique. Access the complete course and earn ASCLS P.A.C.E.-approved continuing education credits by subscribing online.

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Basic Tissue Sampling and Use of Tissue Marking Inks

Marking the tissue edges aids in the identification and correct orientation of the tissue pieces during embedding. It also assists in the correct placement of the intended surface toward the face of the block, which is the first surface to meet the microtome blade.
Tissue markers must:
  • Be insoluble in fixative solutions, processing solutions, and the embedding media
  • Remain on the surface to be marked and not penetrate too far into the tissue interior
  • Not react with histologic stains or be over applied to obscure cells or tissue layers
  • Be notably visible both macroscopically and microscopically
Some examples include India ink, silver nitrate, and various artist pigments. Different tissue marking inks may be applied to mark anatomic or surgical landmarks. This will help orientation both during gross dissection, embedding, and in the final histologic section.
  • The ink may be applied to color the entire outside perimeter of the specimen, or may be used selectively, using single or multiple colored inks.
  • The application color and location will typically be dictated into the gross description.
  • It is recommended to try to avoid red ink, since it may be difficult to see. Black or bright blue ink is often preferred.
Ink marking examples include:

Tissue TypeExample
Small lesions present in a larger section of tissue
  • The lesion may only be visible on one "face" or plane of the section. In this case, one side of the tissue can be inked and specific instructions should be provided such as "embed with inked tissue surface up."
  • Note that most histologists will want to relate any directional instructions to the block face, which is the surface that will meet the microtome blade first.
Tubular structures
  • It is sometimes helpful to submit the entire tube (vas deferens, temporal arteries, fallopian tubes) in the tissue cassette, with instructions to cut cross-sections before embedding.
  • The lumen end can alternatively be dipped in tissue ink, to more clearly mark the opening for very tiny tubes. The lumen MUST be visible in the final section.
Multiple fragments
  • The fragments may be inked on one edge, but should be embedded so that all pieces are kept in the same plane or level in the block so that one complete, representative section can be obtained.