JMLAB Research Histology lab
We are researcher oriented, servicing clients in the Salt Lake City area and beyond.

New clients are required to set up an account before submitting to JMLAB Research Histology.
See below for more information


Projects can be dropped in our drop-off box during business hours. If you have fresh tissue for a frozen project, please email the lab (aphistologyresearch438@aruplab.com) to coordinate a time to drop-off.

Research Histology does not provide supplies, gross specimens, cassette samples, or transfer formalin-fixed tissue to 70% ethanol solution in which we require all projects to be submitted

Research Histology—JM-Laboratories
Huntsman Cancer Hospital

1950 Circle of Hope Drive Room N3970
SLC, UT 84112
Mon-Fri 8a.m.—4p.m.

Phone: 1-801-213-4272


For Immunohistochemistry staining, please contact Leslie Rowe at leslie.rowe@aruplab.com

JMLAB Client ID Account Setup

All clients requesting Histology Research services and approval for Immunohistochemistry stains through JMLAB are required to set up an JMLAB Client ID (account). Please follow the detailed instructions below to ensure we are in compliance with regulatory bodies governing our operations.


If you are working with animal samples only, the process for setting up an JMLAB Client ID takes approximately 8-10 business days.;

Please fill out and submit the following form:

Once your account set up is complete, you will receive a custom JMLAB requisition to submit your specimens to Histology Research.


If your project requires the submission of HUMAN specimens, you must apply for an exemption from electronic (EPIC) ordering.  Please follow the instructions below:

  1. To request an JMLAB electronic (EPIC) ordering exemption or the creation of an Alias medical record, please save the form provided Exclusion Research Data Procedure (PDF) with the IRB number in the file name, complete the form, and email to the CRCE Officer with Compliance Services at the University of Utah. The compliance Office will review and respond within five business days.

This procedure is not defined by JMLAB, rather by the Clinical Research Compliance and Education office (CRCE).  We cannot set up an account for processing human specimens without this exemption approval.

Once you have gone through the steps above, you will receive a notification that your exemption has been approved. This information along with the UU Client Account Information form will be used to set up a research account for you here at JMLAB. Once your account set up is complete you will receive a Custom JMLAB requisition to submit your specimens.

JMLAB Research and Development Immunohistochemistry STAINS

If your project requires additional Immunohistochemistry staining, please follow the instructions below:

Fill out the form entitled Proposed Immunoperoxidase Research Studies and you will be notified if your project has been approved
Services Provided

Arranged by frequency that service is provided

Decalcification—Our lab offers decalcification services.  All tissue containing calcium (bone, bone marrow, etc.) must be submerged in a decal solution prior to processing & embedding until tissue is pliable. Specimens containing calcium cannot be cut after paraffin embedding. Un-decalcified tissue will exhibit cutting artefact and will most likely stain poorly. “Tissue containing calcium must undergo calcium removal before embedding unless specific studies requiring un-decalcified bone are requested” (Carson: 461).

Processing—An automated protocol that involves running tissue through a vacuum infiltration processing machine which replaces all water present in the tissue with paraffin wax in order to stabilize the tissue and make it amenable to cutting.

Paraffin embedding—The process of orienting warm tissue samples into hot paraffin wax molds which are then cooled until the paraffin block is solid. Tissue is embedded in the smallest size mold appropriate for the tissue size. Embedding instructions provided by the client, guide lab staff on how to orient the tissue samples so that the area of interest is sectioned correctly.

Cellblocks—Sometimes collections are of 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 cell may be lost during processing.

Punches—Used in assembling a tissue microarray or for simply examining a small piece of representative tissue. Delivered in an Eppendorf tube.

Shaves/scrolls—Often used for DNA extraction. A shave/scroll is cut in a specific way such that the “section” turns out as a scroll. Shave/scrolls are 10 μm or thicker and delivered in an Eppendorf tube.

TMA (Tissue Microarray)—Many small representative tissue samples are extracted from different paraffin donor blocks and re-embedded into a single recipient (microarray) block at defined array coordinates. A microarray block may contain dozens of these cylindrical tissue cores. After sectioning, a microarray slide is amenable to high throughput analysis of multiple specimens at the same time (Jawhar, 20182).

Repair broken slides—Slides with clean breaks (not shattered) can be repaired.

Wax-dipped slides—This process curbs oxidization and is performed when slides will be kept for some time before testing is done.


Arranged topically

Sectioning—After a specimen is embedded into a paraffin wax block, it can be sectioned on a microtome by a histologist All sections are initially unstained. We can cut as many sections from a block as necessary, up to depletion of the block. Possible ways to section a block include:

  • Leveling, in which a section is obtained from the surface of the block, and then from another plane several hundred microns in (or however deep you'd like to go).
  • Cutting unstained through a whole block. This produces a lot of slides.
  • Cutting along certain planes of the tissue. The clients need to specify this in the instructions for embedding so that the plane you want cut is embedded toward the bottom of the embedding mold. This is can be indicated by inking the surface you want cut first.

Cryosectioning—Once a fresh specimen is embedded in OCT, it can be cut on a cryo-microtome. Orientation guidelines are parallel to regular microtome sectioning. All sections are initially unstained. Various stains can be applied.

Special Staining
Arranged alphabetically

AFB (Acid-Fast Bacilli—Zeil-Neelsen Method)

  • Acid-fast bacteria (e.g. mycobacterium) exhibit acid-fastness, that is, they “stand fast to” or resist acid and/or ethanol based decolorization during the staining process.
  • Acid-fastness is a physical property of the cell. An acid-fast stain is used to identify acid-fast mycobacteria in tissue sections (Carson: 226 1).
  • Acid-fast bacteria of interest are pathogenic to humans.
  • In general, acid-fast stains allow bacteria to be divided into acid-fast and non-acid-fast groups (Carson: 222 1).
  • 4-5 μm.

Alcian Blue, pH 2.5 stain

  • Demonstration of acid mucopolysaccharides (Carson: 145 1).
  • May be used in the diagnosis of diseases such as mucopolysaccharidosis.
  • 4-5 μm.

Alcian Blue, with hyaluronidase digestion

  • For differentiation of epithelial and connective tissue mucins (Carson: 147 1).
  • Bovine testicular hyaluronidase digestion highlights mucosubstances containing hyaluronic acid and chondroitin sulfates A and C (Carson: 148 1).
  • 4-5 μm.

Alcian Blue, with PAS

  • Differentiation between neutral and acidic mucosubstances; this procedure is used in many laboratories today for the detection of intestinal metaplasia (Carson: 148 1).
  • The alcian blue technique stains the acidic mucosubstances, whereas the PAS stains the neutral mucosubstances (Carson: 148 1).
  • 4-5 μm; sections of kidney should be cut at 2-3 μm.

Aniline Blue

  • When used alone, aniline blue is a general stain used for broad differentiation of tissue histology. Hence, it is primarily used for slides to be scraped of tumor for molecular testing.
  • Aniline blue or its constituents are used to stain collagen, as the fiber stain in Masson’s trichrome (HT-PROC-4441).

Auramine rhodamine stain

  • Used to detect mycobacterium tuberculosis or other acid-fast organisms (Carson: 230 1). While the AFB stain is more specific for acid-fast organisms, Auramine rhodamine is more affordable and sensitive and so is frequently used for initial screening (Kommareddi 3).
  • 4-5 μm.

Bielschowsky Method Stain

  • Demonstrates nerve fibers and the presence of neurofibrillary tangles and senile plaques in Alzheimer disease. It is typical for some neurofibrils to result as aging occurs, but in Alzheimer’s tremendous numbers of neurofibrils develop (Carson: 202 1).
  • 8 μm.

Brown-Hopps Modified Gram Stain

  • For demonstrating gram-negative and gram-positive bacteria in tissue (Carson: 231 1). The walls of gram-positive bacteria retain the initial crystal violet dye, whereas the walls of gram-negative bacteria will decolorize to accept a counter-stain. In this way the two types are differentiated.
  • In general, gram stains allow bacteria to be classified as gram-positive and gram-negative organisms (Carson: 222 1).
  • 4-5 μm.

Colloidal Iron

  • Demonstrates carboxylated and sulfated mucopolysaccharides and glycoproteins, which absorb colloidal ferric ions at a low pH (Carson: 149 1).
  • 4-5 μm

Congo red

  • Used to demonstrate amyloid deposits in tissues such as kidney, spleen, and liver where diseases such as amyloidosis are suspected.
  • 8-10 μm (sections not in this range may not show the apple-green birefringence).

Elastin-van Gieson stain (Verhoeff-Van Gieson elastic stain)

  • Elastic fiber techniques are used to demonstrate pathologic changes in elastic fibers. These include atrophy, thinning, or loss of elastic tissue that results from arteriosclerotic developments as well as reduplication, breaks, or splitting of elastic tissue as a result of other vascular diseases. Demonstrating normal elastic tissue and identifying tumor invasion of elastic tissue is another use of elastic fiber techniques (Carson: 168 1).
  • 4-5 μm.

Fites Acid Fast Stain

  • To detect the presence of mycobacterium leprae (causative organism of leprosy) in tissue selections. The lipoid capsule of the organism takes up carbol-fuchsin and resists decolorization with dilute mineral acid (Carson: 228 1).
  • 4-5 μm.

Fontana Masson Silver Stain

  • Used to demonstrate argentaffin substances such as melanin, argentaffin granules of carcinoid tumors, and some neurosecretory granules (Carson: 260 1). Certain tissue components have the ability to bind silver from a silver solution and to reduce it to visible metallic silver without the aid of a reducing agent.
  • 4-5 μm.

Giemsa Stain (Modified)

  • In general, Giemsa stains simply screen for the presence of bacteria (whether acid-fast or not, and whether gram-positive or gram-negative) (Carson: 127, 222 1).
  • Typically, however, the Giemsa technique is used in the identification of helicobacter pylori in tissue sections (Carson: 233 1).
  • 4-5 μm.

GMS (Grocotts Modification of Gomoris Methenamine Silver)

  • The demonstration of fungus in tissue sections (HT-PROC-4419).

H&E (Hematoxylin & Eosin)

  • We use a Modified Harrison Hematoxylin along with Eosin Y. Hematoxylin dyes the nucleus, while Eosin dyes the cytoplasm. General staining method for examining morphology of all types of tissue.

Iron Stain (Mallory's method)

  • To demonstrate excessive amounts of ferric iron in tissue sections (HT-PROC-4423). Excessive amounts of iron found in hemochromatosis and hemosiderosis as deposits in the liver and pancreas can cause significant damage to the tissue. Normally found in the spleen and bone marrow.

Jones (Jones' modification for basement membrane)

  • To demonstrate basement membrane, primarily in kidney tissue sections (HT-PROC-4424).

Luxol Fast Blue (LFB)

  • Demonstration of myelin in tissue sections. When an axon degenerates, the myelin covering breaks down into simpler lipids that will be removed eventually (Carson: 212 1).
  • 10-15 μm

Masson Trichrome

  • Trichrome stains are frequently used to differentiate between collagen and smooth muscle in tumors and to identify increases in collagenous tissue in diseases such as cirrhosis of the liver (Carson: 162 1).
  • 4-5 μm

Melanin Bleach

  • When melanin pigment is present in large amounts, cell detail may be obscured. Also the ability to be bleached, serves as an identifying factor for melanin. Melanin is bleached by oxidizing agents. Agents used in the oxidizing process include acidified potassium permanganate (HT-PROC-4429).


  • Staining of epithelial mucin in tissue sections (Carson: 1421).
  • 4-5 μm

Nissl Cresyl Violet

  • Identification of neurons in tissue sections, or demonstration of the loss of Nissl substance (chromatolysis). This loss occurs when the axons are transected, injured, or destroyed. This is a reversible change in response to axonal injury and is apparently related to the need for the cell to increase protein synthesis as the cell attempts to regenerate a new axon. When the need for increased protein synthesis is ended, the Nissl substance will return to normal. However, if the axon is injured very close to the cell body the neuron may just disappear (Carson: 195 1).
  • 6-8 μm

Oil Red O

  • The oil red O method is used to demonstrate neutral lipids in frozen tissue sections. Fat occurring in an abnormal place such as fatty emboli that may develop after either a bone fracture an injury that crushes a fatty body area may be demonstrated. The fat stain may verify that the emboli caused death. Degenerating material containing fat, such a cell membranes or myelin, may coalesce into fat droplets that are demonstrable with fat stains, and tumors arising from fat cells (liposarcomas) can be differentiated from other types of tumors (Carson: 184 1).
  • 10 μm. Paraffin sections cannot be used because dehydrating and clearing agents dissolve the fat. If free floating sections are not used, then sections of fixed tissue should be picked up on coated, charged, or subbed slides.

PAS (Periodic Acid Schiff)

  • Demonstration of polysaccharides, neutral mucosubstances, and basement membranes (Carson: 137 1). Materials colored by the periodic acid-Schiff reaction are said to be PAS-positive. This reaction will demonstrate glycogen, mucin, reticulum, basement membranes, and pituitary basophil granules (HT-PROC-4434).
  • 4-5 μm


  • For demonstration of fungus in tissue sections, e.g. pneumocystis and aspergillus.


  • To demonstrate glycogen in tissue preferably using parallel slide comparison (HT-PROC-4433) (Carson: 139 1).
  • 4-5 μm

PTAH (Phosphotungstic Acid Hematoxylin)

  • Demonstration of glial fibers (Carson: 207 1).
  • 6-8 μm


  • Following are the major steps in the ammoniacal silver method for reticulin: oxidation, sensitization, exposure to the silver solution, reduction, toning, and removal of unreacted silver, appropriate counterstaining. Reticulin is a connective tissue which EM studies have shown to be young collagen or a small bundle of collagen. Reticulin fibers are normally found throughout the body -- a healthy liver will show well define strands of reticular fibers, but a necrotic or cirrhotic liver will show a discontinuous pattern (HT-PROC-4436).

Rhodamine (copper)

  • To demonstrate copper in tissue sections. Rhodanine demonstrates the protein to which copper binds rather than the copper itself (HT-PROC-4411).

Spirochetes and Legionella: Steiner-Steiner

  • Spirochetes are spiral-shaped bacteria. Their size, shape, and flagella vary according to the genera. Treponema cause syphilis, Yaws, and Pinta diseases. Borrelia includes Lyme disease. Leptospira, Campylobacter pyloridis (heliobacter), Legionella pneumphila bacteria’s, and cat scratch disease are also stained with this technique (HT-PROC-4437).

Toluidine Blue

  • The demonstrations of mast cells in tissue. Mast cells play a key role in inflammation, and allergic reactions, are implicated in the pathology associated with autoimmune disorders, and are found in mast cell tumors (mastocytomas) common in dogs and cats and rare in humans (Carson: 188 1).
  • 4-5 μm

Von Kossa (Calcium)

  • Von Kossa has shown that calcium phosphate can be demonstrated by means of silver nitrate (HT-PROC-4440).
Immunohistochemistry Staining

Immunohistochemistry staining is provided by Research Histology through JMLAB’s Research and Development department. See the Submission Guidelines page for instruction on submitting projects intended for Immunohistochemistry staining.

Numerous Immunohistochemistry stains are provided by JMLAB Research and Development. Please contact Leslie Rowe at leslie.rowe@aruplab.com for more details on Immunohistochemistry staining.

Works Cited

Carson, Freida L.; Hladik, Christa (2009). Histotechnology: a self-instructional text. American Society for Clinical Pathology Press: Hong Kong. Print.

Jawhar, Nazar M.T. “Tissue Microarray: A Rapidly Evolving Diagnostic and Research Tool.” Annals of Saudi Medicine 29.2 (2009): 123–127. PMC. Web. 17 July 2018. URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813639/

Kommareddi S.; Abramowsky C.; Swinehart G.; Hrabak L. (1984). "Nontuberculous mycobacterial infections: comparison of the fluorescent auramine-O and Ziehl-Neelsen techniques in tissue diagnosis". Human Pathology15 (11): 1085–1089. Doi: 10.1016/S0046-8177(84)80253-1PMID 6208117.

Submission Guidelines

FFPE Submissions

Not yet formalin-fixed or paraffin embedded
Before submission client needs to:

  • Formalin-fix tissue for proper time duration1
  • Place specimens in cassettes and label with identifiers2
  • Complete individualized requisition form3
  • Submerge specimens in 70% ethanol holding solution


  • Place project in drop-off box along with completed requisition form

Already formalin-fixed and paraffin embedded
Before submission client needs to:

  • Complete individualized requisition form3


  • Place in drop-off box along with completed requisition form

Submissions for Immunohistochemistry Staining (FFPE Only)

Not yet fixed or paraffin embedded
Before submission client needs to:

  • Formalin-fix tissue for 48 hours (protocols are optimized for 48 hours; protocol modifications will be charged an extra fee)
  • Place specimens in cassettes and label with identifiers2
  • Complete individualized requisition form3 – make sure to check the box for Immunohistochemistry stains by JMLAB Research and Development


  • Transport samples to Research Histology in 70% ETOH holding solution
  • Bring samples to Research Histology promptly after submerging in 70% ETOH so as to limit time in ETOH, which can affect Immunohistochemistry staining quality

Immunohistochemistry Staining Submission Note:

Strongly preferred that samples be sent and cut in Research Histology on the appropriate Immunohistochemistry slides

Already formalin-fixed and paraffin embedded
Before submission client needs to:

  • Complete individualized requisition form3


  • Place in drop-off box along with completed requisition form

Immunohistochemistry Staining Submission Note:

Strongly preferred that samples be sent and cut in Research Histology on the appropriate Immunohistochemistry slides

Frozen Submissions

Recently collected fresh specimens
Before submission the client needs to:

  • Call Research Histology to arrange drop-off time 4
  • Complete individualized requisition form3
  • Wrap fresh tissue in saline-moistened gauze
  • Place specimens on ice


  • Give project to laboratory technician along with completed requisition form

Specimens that have been paraformaldehyde-fixed 5 but are for frozen sectioning
Before submission the client needs to:

  • Call Research Histology to arrange drop-off time 4
  • Complete individualized requisition form3
  • Rinse paraformaldehyde-fixed5 specimens thoroughly in distilled water (15 minutes recommended)
  • Place specimen in 3% sucrose solution until tissue sinks
  • 10% sucrose solution until tissue sinks
  • 20% sucrose solution until tissue sinks
  • 30% sucrose solution until tissue sinks
  • Place each specimen in a 30% sucrose solution in individual vials


  • Give project to laboratory technician along with completed requisition form

1 The proper time for for neutral buffered formalin-fixation depends on 1) the size of the tissue and 2) the type of tissue.

Determining the amount of time to fix tissue is the responsibility of the client. For more on general guidelines, see “Fixation time” in the Terms & Definitions section.

2 Each given specimen needs to be placed in a cassette (see the Recommended Products section for the type of cassette we suggest) and labelled with a unique identifier. A unique identifier should be alpha-numeric (JC546-54) or at least poly-numeric (e.g. 54891-1).

3 The individualized requisition form is the form you were given when you set-up your account. It is  a requisition form that has the client’s account number, project title, and contact information already filled in at the top.

4 Please refer to our Contact Information for our phone number. Please call us to let us know when you’ll be sacrificing and thus when you’ll be able to bring your fresh specimens. We need to know this information as we embed specimens for frozen sectioning in OCT immediately.

5 Note: No formaldehyde We can only embed frozens that have been previously fixed in paraformaldehyde.

Terms, Definitions, and Relevant Submission Guidelines

Italicized words indicate that a separate entry has been made for said underlined word

Fixation & Processing

Autolysis—The process whereby tissue and cells are destroyed or digested by the enzymes normally present in cells (Carson: 367 1).   Tissue not fixed, improperly fixed, or not properly prepared for fixation may be subject to autolysis. Autolysis negatively affects the morphology and character of the tissue, which in turn will impact the quality of any subsequent preparation or analysis.

Biopsy run—Tissue specimens thinner than 2mm (biopsy size) are put through a shortened processing run to prevent damage to the tissue (see routine run). It is recommended that biopsy size tissue be placed in tissue wrap to prevent loss of the tissue during the processing run and to maintain the correct orientation

FFPE— Acronym forformalin fixed, paraffin embedded.

Fixative—a chemical that alters tissue by stabilizing protein in such a way that the tissue is resistant to further changes (Carson: 368 1).

Fixation—the stabilization of protein (Carson: 368 1). Formalin, 10  percent, neutral buffered, is the preferred universal fixative for histology preparation. Tissue that has undergone fixation is referred to as being “fixed.” Tissue specimens of different sizes require different times to fixate.
Note:we require that fixation be completed and placed in a holding solution before submission.

Fixation time—for best fixation results, tissue should be placed in fixative immediately after excision or surgical removal (that is, after loss of blood supply). The sooner, the better.

The duration of fixation is also important. Adequate fixation improves the imperviousness of tissue to the effects of subsequent denaturing agents during processing. It also reduces the likelihood of embedding or cutting artefacts, which impact histological analysis. For larger specimens, Dapson found that artefact free specimens “could only be produced after a minimum of 30 to 40 hours of fixation with [10  percent] neutral-buffered formalin” (Carson: 6 1). The American Society of Clinical Oncology and the College of American Pathologists recommend a minimum of 6 hours and a maximum of 48 hours fixation time in 10% neutral-buffered formalin for biopsy sized specimens (Carson: 6 1).

In any event, the duration of fixation depends on both the size and type of tissue. Given the wide variety of submissions we receive both in terms of size and type, no definitive answer can be provided as to how long tissue should be fixed—it is up to the submitter to determine how long their tissue needs to be fixed. If you are unsure or do not know where to look, please ask.

Holding solution (aka preservative)—a chemical solution that suspends or “holds” fixed tissue in its stabilized state, that is, kills bacteria and molds, renders enzymes inactive, and neither shrinks nor swells tissue (Carson: 370 1). A holding solution does not modify or alter tissue like a fixative does. A 70 percent ethanol solution is the preferred holding solution for any tissue that will be paraffin embedded.
Note: after tissue has been fixed, place tissue in the holding solution. We require that all submissions be already fixed and submitted in the holding solution.

Identifier (aka Label aka Block ID)—cassettes containing tissue must be submitted having an identifier labelled onto the top of the cassette. The identifier is a unique alphanumeric tag associated with the tissue specimen inside the cassette. The best identifiers contain both letters and numbers as this prevents blocks from getting mixed up (for instance, two different people from the same lab make two submissions with the identifiers “1”, “2”, “3”, etc.). The identifier must be written with pencil onto the cassette body—writing in pencil is necessary since other materials tend to wash off during processing. The identifier(s) are then listed on the requisition form associated with the specimen(s) to ensure that all specimens are accounted for and subsequently for billing purposes.

Processing—refers to how tissue is prepared for embedding and cutting. Processing involves dehydration, clearing, and infiltration of the tissue. Dehydration removes water from the tissue with alcohol; clearing renders the tissue transparent and dealcoholizes the tissue in order to make the tissue receptive to the infiltrating agent; infiltration involves permeating the tissue with a supporting medium such as paraffin wax (Carson: 33, 35, 37 1).

Routine run—tissue specimens other than those for a biopsy run are put through an 8 hour “routine” processing run that caps off the fixation process and prepares the specimen for embedding and cutting.

Vacuum infiltration – a stage in the processing run that infiltrates tissue with a supporting medium, that is, paraffin wax. Vacuum infiltration improves the general diffusion of the supporting medium.

Tissue wrap—special paper in which small tissue specimens are wrapped to avoid loss of specimen during processing and maintain orientation, etc.; good tissue wrap will retain very small tissue aggregate, be lint free, and be permeable to reagents during the processing cycle. Histowrap® by Obex is the preferred brand.
Note: when wrapping tissue in tissue wrap, moisten the tissue wrap with fixative prior to tissue placement. This will prevent drying artefact and the tissue from adhering to the tissue wrap.

Whole mounts—an extra-large cassette that is used for embedding very large tissue.

Embedding & Orientation

Bottom of cassette – the bottom of the cassette is the side opposite of the cassette lid.

Bottom of mold—the bottom of the mold is the side facing down when embedding, and which is cut first on the microtome.

Cassette—the cassette is a plastic container that is used to hold identified specimens. It has two parts: the cassette body and the cassette lid. Both parts have small holes which allow for the fixative and holding solution to associate with the tissue inside the cassette.
Note: we require that all specimens be submitted in labelled cassettes (use pencil) and that each cassette label is listed on the accompanying requisition form.

Cell blocks—rather than a piece of tissue, sometimes collections are of a concentration of cells. We accept cell aggregate submissions for processing, embedding, and sectioning.
Note that cell aggregate needs to be packaged in Histowrap® —otherwise, cell chunks will be lost during processing.  

Inked margins—inked tissue indicates where cutting is to be performed first.

Lumen – 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: 43 1); examples of tissues routinely embedded on edge include cysts, gallbladder, specimens with epithelial layers (e.g. skin), and colonoscopic, endoscopic, & cervical biopsies.

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: 43 1); this embedding orientation is routinely applied to tissues with a lumen such as veins, the appendix, and 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 while embedding and is closest to the embedder; it is the side opposite of where cutting will first be performed.

Swiss rolls – refers to arranging a colon in the shape of a Swiss roll, i.e. rolling the material around in circles on itself. Embedding colon in the shape of a Swiss roll puts the outer, middle, and inner parts of the colon on edge.


Cutting – a microtome is used to cut sections from a FFPE tissue block. Typical section thickness is 3-5µm. For contrast, a typical piece of paper is 100µm thick.  Cutting is often referred to as sectioning.

Levels – refers to 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. 50µm) and then another section is collected. This process can be repeated iteratively until the block has been exhausted of tissue.

Sample—used as 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 off of a FFPE block from a microtome.
Note that multiple sections can be placed on one slide, if applicable.

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

Frozen Specimens: Preparation & Embedding

Cryomolds—cryomolds used to embed frozen specimens in OCT. We use three different mold sizes to accommodate different tissue sizes: astandard size (25mm x 20mm x 5mm), an intermediate size (15mm x 15mm x 5mm) and a deep size (surface size is slightly larger than the standard, and depth is for particularly thick pieces of tissue).

Cryoprocessing – refers to the process of preparing frozen tissue for embedding and cutting. 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 – stands for “Optimal Cutting Temperature” compound, this admixture of water-soluble glycols and resins is used to embed tissue specimens prior to frozen sectioning on a microtome-cryostat.

Frozen Specimens: Cutting/Sectioning

Frozen Sectioning—frozen specimens in OCT are cut on a cryo-microtome, anywhere from 3 μm to 30 μm.

Slide—slides are made of glass and serve as a mount for tissue sections. Sections stick to a slide when the slide is charged.

Coverslip—this is a plastic wrap that goes around a stained slide to protect it from environmental damage.
Administrative Terms

Project Order—refers to the totality of a submission. This phrase is more often used in accounting and billing contexts. The difference between the terms submission and project order is pragmatic: whereas “submission” is used in reference to the physical handing in of materials, the phrase “project order” is used when referring to the non-physical aspect of a submission, that is, it underscores the fact that the submission is an “order” made by the client. 

Requisition Form—the official order form handed in along with asubmission that includes the client number and project title, contact information, number of cassettes submitted, submission instructions, list of identifiers (block IDs), relevant order instructions, and additional comments.

Specimen(s)—refers to the tissue itself. May also refer more broadly to the tissue and accompanying paraphernalia, such as the tissue along with the cassette, in Histowrap® , etc. 

Submission—refers to all the components of a project order: the specimens, completed requisition form, list of specimens, and any other accompanying materials. The difference between the terms submission and project order is pragmatic: whereas “submission” is used in reference to the physical handing in of materials, the phrase “project order” is used when referring to the non-physical aspect of a submission, that is, it underscores the fact that the submission is an “order” made by the client. 

Other Terms

Artefact—Carson describes an artefact as any “structure or substance not normally present but produced by some external force or action” (Carson: 366 1). Examples include knife/cutting lines, misshapen cell morphology, and tissue floaters. Proper preparation and fixation are paramount for reducing associated artefacts as these steps cannot be redone, whereas samples may be re-embedded if air bubbles are present or another section obtained if a preventable knife line is present.

Core punch – a “core punch” refers to punching out a cylinder of tissue from a FFPE tissue block. Also referred to as “punch ” or “tissue punch.” It is different from “core” which refers to a needle core biopsy . The standard size of a core punch is 2mm, but we also offer 1mm sized punches upon request. If a different core punch size is needed (e.g. 3mm, 5mm, etc.) you will need to provide the punching tool. For research projects using archival human tissue, the approval of the medical director is required.

Needle core (biopsy)—refers to cores of tissue taken with a needle during a biopsy. Not to be confused with core (punch) which is taken from a FFPE tissue block.

Tube—a tube refers to the container that may hold a core punch or a scroll/shave.

Scroll/shave—scroll and shave are interchangeable terms that refer to sections cut in such a way that the section curls up in the shape of a scroll. Often used for DNA extraction.

Works Cited

Carson, Freida L.; Hladik, Christa (2009). Histotechnology: a self-instructional text. American Society for Clinical Pathology Press: Hong Kong. Print.

Pricing and Products


University Price

List Price

Process and embed (PE) only $2.89 $20.00
Process, embed, 1 unstained slide $5.20 $56.00
Process, embed, 1 H&E slide and stain $6.55 $59.00
1 unstained slide only (no PE) $2.00 $20.00
1 H&E stain only (no PE, no slide) $0.99 $20.00
1 H&E slide and stain only (no PE) $3.00 $25.00
Freeze and embed only $2.69 $25.00
1 frozen slide only (no PE) $4.00 $30.00
Freeze, embed, 1 frozen slide $6.69 $5