Starting pathology

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Author: Mikael Häggström

Using this handbook

The goal of this handbook is to make a new pathology trainee able to properly handle at least 80% of cases that are expected at an average general pathology department, including the exclusion of the most pertinent differential diagnoses thereof.

It is recommended to scroll quickly through this handbook to get an idea of its content, and then keeping it at a known location for whenever information is needed for a corresponding patient case. It is not recommended to memorize its content indiscriminately. Other doctors and even laypersons can look up diseases and conditions themselves, including pathology characteristics, without the need for a pathologist consultation, so the expertise of memorizing such readily available information is expendable. In a world where diseases and conditions can readily be looked up, a major skill that distinguishes a pathologist from any person with Internet access is mainly the ability to identify and put words to findings on microscopy or other non-written results. Another major skill is to be able to deal with unusual or equivocal presentations. Unusual or equivocal presentations of very common diseases and conditions are still generally more common than rare diseases, and constitutes a major workload in everyday pathology practice. However, most textbooks still give disproportionately large room for rare diseases compared to such presentations. Nevertheless, strive to master the common conditions (including the most common pitfalls) before diving into the uncommon. Specialists and subspecialists may already have learned the common conditions, at least in their subspecialty, and they will often distract you from this pursuit by presenting rare conditions to you, because that is interesting to them, but do not spend excessive time or mental effort on such rare conditions during your first years.

What a pathologist needs to memorize

The best method for memorization is generally through repeated exposure in everyday practice, but the following things are most important for a pathologist to focus on memorizing:

  • Emergent pathology, mostly relating to intraoperative or frozen section consultations. This includes information that usually cannot be timely looked up on the Internet when needed.
  • Main pitfalls: Most common and dangerous situations where a pathologist may not recognize the need to look something up further or ask a senior colleague.
  • Patterns and signs which can be seen grossly or under the microscope. It confers the ability to translate visuals into words that can be looked up if needed.
  • Knowledge of where to find information for various situations. It includes which person or which search engine is most useful for various clinical situations. Google is generally an appropriate search engine, but sometimes more specific or comprehensive databases are necessary, such as for example ClinVar to look up the pathogenicity of specific genetic variants. The chapter will include a directory of major databases and external guidelines.
  • Proficiency in diagnosing equivocal or borderline cases where readily available sources and evidence usually deal with discrete and specific disease entities and subcategories thereof.  Thus, in the question sections, many questions will be in the format of displaying readily available facts about diseases, including their typical immunohistochemistry patterns, but with equivocal or borderline case presentations.
  • Having an idea of one’s unknowns; being aware of unfamiliar fields. For example, a pathologist generally does not need in depth knowledge about cases that are generally sent out to specialized centers (such as pediatric musculoskeletal oncology), as long as that pathologist is aware of lack of knowledge in that field.
What you need to memorize.jpg
  • Dealing with Internet denialists and their exams. With the ease of access to pathology information on the Internet through smartphones and computers, those studying to for everyday practice as a pathologists should not spend time memorizing what can essentially always be conveniently and timely be looked up in times of need. The topics listed above are already immense enough to cover a lifetime of learning. Nevertheless, the path to pathology certification includes one or more exams, whose questions are largely made up of people who still do not acknowledge the access to the Internet in everyday pathology practice, and therefore this curriculum also includes this chapter.

Emergent pathology

Surprise frozen sections

While most frozen sections can be predicted from schedules of the operating room and thereby be looked up beforehand, this chapter deals with the most common ones that do not offer such preparation time, thus indicating memorization of how to handle them.

(Gather most common situations.)

Other frozen sections

Although these are generally given on schedules of the operating room, any pathologist may end up suddenly covering for another one, and subsequently be presented with the frozen section case without having had the time to look it up beforehand.


Also largely a directory of external guidelines and databases.

Non-emergent pathology questions


Which of the following situations does not have comprehensive guidelines available online?


Ask what are the main locations to look for infection in a specific autopsy case.

Provide algorithm of gram stain etc. and table of main bacteria by various locations.

Where to find information


Provide genetic variant in long format.

- Which database is the best to use to look up the pathogenicity of this variant?

 - ClinVar (correct)

 - gnomAD (population frequencies)

 - PolyPhen (likelihood of protein damaging)

 - PharmGKP (associated treatments)

- In ClinVar, what would you enter

 - A1708V (then BRCA1)

Dealing with Internet denialists and their exams They take pride in for example memorizing the chromosome locations of even rare mutations, but when being called in for a frozen section of even relatively common specimens such as brain, lung or skin tissues, they may not know how to differentiate even the most common 90% of diagnoses.

An Internet denialist who has memorized something may assume that pathology trainees should memorize it as well, and entire lectures may largely consist of rants of such items. In reality, when something is encountered and looked up something enough times, it will generally get memorized. It is generally more efficient to let time tell which situations will be common versus uncommon, rather than trying to memorize knowledge for even uncommon situations.

An internet denialist exam is basically any exam wherein the examiner does not have access to the Internet, and typically is not allowed to ask colleagues either. Since these two resources are fundamental in everyday practice, such exams are thereby of a different dimension compared to everyday pathology practice.

Exam studying

For a multiple choice exam like the American boards, you don't actually need to know the answer, but just have a feeling of what is the most likely answer among the choices.


Author: Mikael Häggström [notes 1]

General notes edit

Within an hour after removal from the body,[1] tissue samples should generally be placed in vessels with the correct fixing solution, with a volume that allows them to lie freely in the solution.[2] The standard fixation fluid is generally 10% neutral buffered formalin, which is roughly equivalent to 4% formaldehyde.[3]

The main exception to using formalin are mainly:

  • A tophus or other specimen suspicious for gout versus pseudogout should be sent in alcohol or dry, since formalin will dissolve the crystals.
  • Lymph nodes (or other lymphoid aggregates) with a suspicion of lymphoma, where samples are generally put in a special solution for flow cytometry.
  • Products of conception with a need to take samples for genetic testing.


  1. For a full list of contributors, see article history. Creators of images are attributed at the image description pages, seen by clicking on the images. See Patholines:Authorship for details.

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Gross processing

Author: Mikael Häggström [notes 1]

General notes edit

Following are general notes on selection and trimming in pathology.


On this resource, the following formatting is used for comprehensiveness:

  • Minimal depth
  • (Moderate depth)
  • ((Comprehensive))
Other legend

<< Decision needed between alternatives separated by / signs >>
{{Common findings / In case of findings}}
Link to another page

Before cutting

  • Confirm that the patient identity on the specimen container matches the identity that will be applied to the gross description and cassettes. {{If the referral or requisition form is available, confirm the patient identity on that one as well.}}
For unclear or potentially ambiguous handwriting (here "Right" or "Left" renal stone), look at the referral or requisition form ((and the medical record if available)).
  • (Check for any discrepancy between the specimen description on the container and on the referral or requisition form, such as left versus right.)
  • Generally measure estimated volume or 3 dimensions for samples greater than 0.4 cm in greatest dimension.[notes 2]
  • Generally weigh entire organs, after having any attached tissue trimmed away if feasible.
  • ((Note the color of the sample, even when unremarkable, but do not linger on deciding it.))[notes 3]
  • Generally, use inking for resection margins where cancer radicality is important. Further information: inking
  • (On fatty or greasy surfaces, apply vinegar to emulsify and remove the fat, dry the specimen and then ink. Otherwise, vinegar can be used either before or after inking to "dry" it.)
  • (Preferably photograph or make a drawing where slices have been taken.)[4]
  • Remove any surgical stitches from samples before microtomy.
  • (At least for larger samples, consider looking for medical imaging or biopsy reports in order to better guide the process.)[5]
  • Fix bone in formalin prior to decalcification. Use reminders so not to forget bone that is decalcifying.


  • When cutting with the longer knives, try to cut in one stroke - do not use like a saw (continuous back and forth)
  • Generally, strive to make slices perpendicular to visible interfaces of relevant tissues.
  • Generelly dissect and inspect the entire specimen, while keeping relevant parts intact enough for presentation to seniors and/or maintaining orientation.
  • Trim tissues for microscopy examination to a thickness of maximum 3-4 mm.[notes 4]

Perpendicular versus en face sections

Perpendicular and en face sections

Two major types of sections in gross processing are perpendicular and en face sections:

  • Perpendicular sections allow for measurement of the distance between a lesion and the surgical margin.
  • En face means that the section is tangential to the region of interest (such as a lesion) of a specimen. It does not in itself specify whether subsequent microtomy of the slice should be performed on the peripheral or proximal surface of the slice (the peripheral surface of an en face section is closer to being the true margin, whereas the proximal surface generally displays more area and therefore generally has greater sensitivity in showing pathology, also compared to perpendicular sections).
  • A shaved section is a superficial en face slice that contains the entire surface of the segment.

Tissue selection

When sampling sections to submit for microscopic examination, whenever you sample from something that looks abnormal, generally try to also sample from the same type of tissue that looks normal.[notes 5]

Biopsy wraps, bags and sponges

Items used for submitting specimens: (Biopsy) wrap, (biopsy) sponge, (tissue processing) cassette and (biopsy) bag.

Put the following types of specimens in bags:

  • Tiny specimens that need to be poured out from their containers.
  • Bloody specimens such as endometrial curettages or products of conception. For products of conception, chorionic villi may otherwise contaminate other specimens. Bloody specimens may stick to wraps, so generally avoid that situation.
  • Friable tissue such as urinary bladder biopsies.

Put the following types of specimens in bags, wraps or sponges:

  • Other tiny specimens
  • ((Any small piece of tissue where there is no leftover specimen to retake sections, since tissues occasionally get lost from cassettes, and the absence of a wrap, sponge or bag in the cassette of such cases points towards a mistake made at gross processing.))

Specimens must be fixed enough to be put on sponges.

By organ or organ system


  1. For a full list of contributors, see article history. Creators of images are attributed at the image description pages, seen by clicking on the images. See Patholines:Authorship for details.
  2. Specifying dimensions in 3 dimensions is generally a waste of time for specimens less than 0.4 cm.
  3. The color is generally of little consequence.
  4. Thicker slices may not become adequately fixated in formalin.
  5. Normal sections from the same tissue helps identifying what is histologically abnormal in the grossly abnormal tissue, versus normal individual variations.

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Evaluation of tumors

  1. REDIRECT Evaluation of suspected malignancies


Author: Mikael Häggström [notes 1]

General notes edit

Following are general notes on reporting in pathology.


Selection and trimming

From the stage of selection and trimming, a histopathology report should preferably include:

  • Case:
  • Patient identification and/or sample number
  • Type of tissue sample as described on container
  • Dimensions of original tissue[6]
  • Directions or other features of any inked surfaces.
  • Generally the weight of larger samples[6]
  • Dimensions of pathologic components[6]
  • Whether the entire specimen or representative sections were submitted.

Microscopic evaluation

  • Specimen chronology, often A, B, C, etc., at least where there are multiple specimens from the same case. With multiple specimens, preferably write out the chronology for all of them first, so that you don't miss reporting any of them later.
  • Specimen type and/or surgery type, such as "appendix, appendectomy", for clarification. This is not necessary at all departments.
  • Findings. This is not always necessary, but should be included if the diagnosis is uncertain. One systematic approach is to describe findings from largest to smallest ones. For example, a description of a tumor can start with the demarcation of the tumor, followed by texture, cell shapes, nucleus shapes and chromatin appearance.
  • Diagnosis or most probable diagnoses.
  • In case of malignancy or suspected malignancy:
  • Depth or most distant invasion of malignant findings.[6] Depending on location, it may need to exclude important pathways, such as vascular, neural and/or through capsules or other layers.
  • Whether the resection is radical or not.


Factors supporting a relatively more comprehensive report, particularly in the inclusion of negated findings:

  • Lack of explanation from existing evidence. For example, an inflamed appendix that fits the medical history does not need detailed mention of harmless incidental findings.
  • Double-reading: If your report is likely to undergo double reading by another pathologist before sign-out, it needs to be more detailed, because the doctor who will do the double-reading then knows that you have looked at those locations.
  • Highly suspected locations, such as given from the referral.
  • Defensive precautions, which appears to be more common among doctors in the Unites States compared to for example Europe.[7][8]

Multiple instances of the same type of pathology (such as lung nodules) can often simply be reported as such, at least with a particular mention of the largest or the most severe example thereof.

Where findings are made, general statements of clearing a region should still be given, such as: "There is a 18.0 cm curvilinear well-healed thin scar in the left thorax. Otherwise, there are no puncture marks or healed surgical scars on the torso." The main exception is for aspects that are barely worth mentioning, in which case the description of the finding may imply that the aspect has been considered in general.


The same word used describing the certainty of findings can refer various probabilities, differing between pathologists as well as clinical situations. The following is a suggestion of words, in an attempt to sort them from most to least probable:

(non-lethal condition) cannot be excluded
not likely
(lethal condition) cannot be excluded

For findings and diagnoses, is preferable to write "negative for..." rather than "no..." to emphasize the possibility of false negative findings.

Synoptic reports

For cancers, generally include a synoptic report, such as per College of American Pathologists (CAP) protocols at However, synoptic reports are generally not needed for tumor metastases.


Whenever possible, give numerical quantities of sizes, rather than descriptions that are subjective (such as "small" or "large") or variable (such as "apple-sized").


The information contained in the reporting sections in Patholines assume that the clinician has requested the exam for the topic of the article at hand, but should be tailored to any particular questions or requests by the clinician. Any relevant findings beyond the issues or questions raised by the clinician should also be mentioned.

The most important findings can be moved to near the top of the report if feasible, but doctors performing subsequent double-reading may prefer a consistent anatomic order.

If a certain grammatical rule has a risk of making the report less clear to the reader, ignore it.

Restrict acronyms/abbreviations to those who are certainly well known among all doctors, such as "cm".[notes 2]

Generally describe what can be seen rather than processes (such as preferring "an abundance of" rather than "proliferation of").

Skin excisions

In skin cancers, "peripheral" or "radial" margins are preferred rather than "lateral".[9][notes 3]

See also


  1. For a full list of contributors, see article history. Creators of images are attributed at the image description pages, seen by clicking on the images. See Patholines:Authorship for details.
  2. Acronyms/abbreviations increase reading speed only if the reader is familiar with the abbreviated terms:
  3. A "lateral" margin may be interpreted as opposite to the "medial margin"

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  1. . Breast pathology grossing guidelines. UCLA Health. Retrieved on 2021-09-09.
  2. Katarzyna Lundmark, Krynitz, Ismini Vassilaki, Lena Mölne, Annika Ternesten Bratel. Handläggning av hudprover – provtagningsanvisningar, utskärningsprinciper och snittning (Handling of skin samples - Instructions for sampling, cutting and incision. KVAST (Swedish Society of Pathology). Retrieved on 2019-09-09.
  3. . Paraformaldehyde, Formadehyde and Formalin. Duke University. Retrieved on 2019-12-17.
  4. Monika Roychowdhury. Grossing (histologic sampling) of breast lesions. Topic Completed: 1 August 2012. Revised: 19 September 2019
  5. . Gross Pathology Manual By The University of Chicago Department of Pathology. Updated 2-14-19 NAC.
  6. 6.0 6.1 6.2 6.3 . An Example of a Melanoma Pathology Report. Melanoma Foundation. Retrieved on 2019-09-24.
  7. Studdert D. M.; Mello M. M.; Sage W. M.; DesRoches C. M.; Peugh J.; Zapert K.; Brennan T. A. (2005). "Defensive medicine among high-risk specialist physicians in a volatile malpractice environment ". JAMA 293 (21): 2609–2617. doi:10.1001/jama.293.21.2609. PMID 15928282. 
  8. Steurer J.; Held U.; Schmidt M.; Gigerenzer G.; Tag B.; Bachmann L. M. (2009). "Legal concerns trigger PSA testing ". Journal of Evaluation in Clinical Practice 15 (2): 390–392. doi:10.1111/j.1365-2753.2008.01024.x. PMID 19335502. 
  9. David Slater, Paul Barrett. Standards and datasets for reporting cancers - Dataset for histopathological reporting of primary cutaneous basal cell carcinoma. The Royal College of Pathologists. February 2019