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Neuropathology Surgical Specimens

Stereotactic and endoscopic CNS biopsies are assessed intraoperatively in the frozen section room. Tiny amounts of diagnostic tissue are utilized for touch imprints and smear preparations. The remainder of the tissue and all intraoperative preparations are to be secured in a plastic container with fixative and transported to the gross room on the 6th floor. If you are carrying the intraoperative smears and frozen sections remember to drop them off in the gross room and then pick the slides up (in the gross room) the next morning after they are labeled with the case number.

  • When a frozen section is performed, be sure to remove the metallic “chuck” holding the OCT block from the Cryostat, and immediately place the frozen block in a formalin container to thaw. Once the block has thawed in the formalin, the metallic chuck should be removed and washed. Chucks are in short supply and should be left in the frozen room. Label the container holding the frozen section with the patient's name and “FS- (part)”. Remember to also label the touch preps/smears/frozen section slides with the adequate surgical pathology number. Otherwise, they will not be filed with the rest of the case. Document start time, finish time, surgical site, diagnosis and participating resident/fellow/attending on the requisition. Check that the correct surgeon is documented and add any additional patient history that was conveyed verbally in the O.R. Add "BBX" if biopsy is small.

Grossing Rules of Thumb


  • Include an adequate gross description as part of every surgical pathology report. Each separately identified tissue specimen submitted for individual examination and diagnosis should have its own gross description. Whether "part" or "all" of the specimen has been submitted for microscopic examination should always be recorded in the gross description as well as any special processing (e.g. erythrosin use, tea bags, etc.).
  • A good gross description includes measurements of the specimen in three dimensions, appearance or color (tan, yellow, white, etc.), consistency (soft, hard, rubbery, fleshy, etc.). Gross lesions, tumors or abnormalities within the specimen should also be described in detail: location within the specimen, if single or multiple, measurements, color, consistency, and if relevant margins of resection, etc.

How Many Cassettes to Submit?


  • For primary brain and meningeal tumors, the entire tissue is submitted unless the specimen is over 5 cm.
  • For known metastatic brain lesions only two or three representative sections should suffice.
  • For large primary tumors (any speciment larger than 5.0 cm in greatest dimension), the "one-block-per-centimeter-of-tumor" rule is acceptable.
  • Be sure to section every specimen and submit samples of everything that looks or feels different.
  • Pieces of cranial bone are usually cut with a bandsaw and representative sections are submitted for decalcification. 
  • For temporal lobectomies, hippocampi or other lobectomy specimens proper orientation is critical. 
  • Open cortical biopsies for "encephalitis of unknown etiology" require special attention.  Give the OR a "heads-up" that at least 1 cubic cm of fresh tissue is required and should contain leptomeninges, gray and white matter, preferably at a sulcal depth.  Save a portion at -80 C and put some in glutaraldehyde for possible future studies/EM.  Section the remainder every 3 mm perpendicular to the gray-white junction, fix for several hours and submit in entirety.


Each block should be identified with a unique number or letter.

Do not give multiple blocks the same identification number or letter. A summary listing the sites from which each identified block is taken should be placed at the end of the gross description. Neuropathology surgicals are submitted to the Histology lab in blue cassettes. Restrict the use of gray cassettes to the rush specimens (aka the Stereotactic biopsies). If a case has a lot of parts please limit the use of gray cassettes to the ones you think need to be out at the Rush times. The current labeling system assigns a number and a letter to each block, the number represents the part (1,2,3, etc.) and the letter designates the many pieces in which that part was divided (1A, 1B, 1C). The plastic cassette should be labeled by the automated cassette labeler starting with the PHS prefix followed by the year, sequential number and part. Be advised and warned that minute fragments of CNS tissue from stereotactic or endoscopic biopsies will be lost during processing if submitted in regular size cassettes. Fragments less than 0.4 cm in diameter should be wrapped in tea bags and submitted in gray cassettes. If small core biopsies are submitted, order blanks up front (BBX) to avoid running out of tissue in subsequent refacing of the block.

Taking pictures.

Err on the side of taking digital images of all gross specimens. Images should be appropriately labeled and a measuring scale provided, preferably in centimeters. Cases with potential medical-legal implications should always be imaged.

Recording in the gross description the fact that margins are inked.

For Neuropathology, margins are only an issue in rare instances (bone, soft tissue and peripheral nerve sheath tumors); primary CNS neoplasms are almost never assessed for margins of resection.

Recording the distribution of tissue for special studies in the gross description.

Always include in your gross description if you are submitting frozen samples for tissue bank, if tissue was utilized for research purposes, and which piece corresponds to which block or cassette.

Consult cases.

The pathology report should include a list of slides, blocks or tissues received from another laboratory, the numbers of the slides and blocks, the referring hospital's identification numbers or letters, the referring hospital's demographic data and the date of the surgical procedure. The neuropathology secretary is responsible for accessioning consult cases and typing a short gross description, including all the above information. Remember that when ordering an H&E on a consult block in COPATH, you MUST change the "initial H&E" to an "RHHE." Unless an RHHE is ordered on a consult block, you will not receive an H&E Also, email histology (Chris Simmons) to notify them that a block has been sent.

Temporal artery biopsies.

Temporal arteries are submitted intact to Histology, the histotechs will serially section and embed the tissue after processing. COPATH automatically generates the Histology protocol for temporal artery biopsies; you only have to run the protocol.

What to do when additional parts from an already signed out case arrive at the gross room.

Confirm that these additional parts come from the same day, same procedure as the already signed out case, then:

  • Step 1. Additional parts should be added to the original case by using the Histology entry/edit activity in CoPath.
  • Step 2. Dictate an amended report to add the gross description and final diagnosis of the additional specimen/s.

Standard sampling of autopsy brains.

The routine sampling of an autopsy brain includes the following sections:

2A. Mid-frontal cortex, left
2B. Caudate, corpus callosum, cingulate gyrus, left
2C. Basal ganglia, left
2D. Thalamus, left
2E. Hippocampus , left
2F. Cerebellum, dentate nucleus
2G. Midbrain
2H. Pons
2I. Medulla
2J. Spinal cord (3 levels)
2K. Pituitary Gland

If no gross pathology is evident the attending may choose to submit routine histologic sections for embedding only, or not to submit any tissue and make the case a “gross only diagnosis.” If sections are submitted for embedding only, enter the cassettes as you normally would in COPATH and in the Stain/Process and block Edit option write “for embedding only” in the comment area next to each block.


Gross description and gross diagnosis of autopsy brains.

You are expected to generate a gross description of the brain(s) you cut within 48 hours. A standard gross of a normal adult brain can be found in the Quicktext library in COPATH.