Goals and Objectives

General Objectives

By the end of this 4 week rotation, the PGY1 Anatomical Pathology (AP) resident is expected to develop an understanding of:

  • The AP resident role in the frozen section suite
  • Principles of specimen opening in the gross room (EPA: TTD#1):
    • Ischemic time in tumours
    • Scout section(s) to mitigate over-fixation
    • Orientation to the gross room with respect to various fixatives and handling of unique specimens ie. Lymphoma protocol
  • Principles of cytology with respect to types of procedures, fixatives and on-site evaluation
    • Adequacy
    • Formalin fixed sample for any case that may require ancillary studies
  • The autopsy process:
    • Valid autopsy consent
    • Personal protective equipment
    • Orientation to the morgue
  • The handling of tissue blocks in histology and immunohistochemistry lab (EPA: TTD#1)

The four week block will be divided as follows:

  • One week of frozen section
  • One week of opening bench/gross room
  • One week autopsy suite
  • 2 days – histology lab and immunohistochemistry lab
  • 2 days – cytology (on-site evaluation)


  • If you anticipate that you will require vacation or CME time during this block, please advise the PD so that this block may be rescheduled to the next available slot.
  • If this is not possible or there is an unexpected absence, it will not be possible to reschedule components of this block at a later time.

For specific goals and objectives please refer to the specific rotation goals and objectives, under the PGY2-PGY5 headings, particularly Autopsy, Cytopathology and the major (core) surgical pathology subspecialty rotations. 

Medical Expert Role

  • The resident will be placed on the daily resident schedule for frozen section and autopsy.
    • The chief resident will coordinate and schedule the appropriate days for histology and immunohistochemistry lab, opening bench/gross room and cytology (on-site evaluation)
  • For frozen section, the resident will be assigned with a senior resident and staff, and will learn the following (EPA: TTD#1, C#13):
    • Compare and contrast frozen sections and formalin-fixed, paraffin-embedded permanent sections, including the advantages and limitations of each.
    • Perform embedding, cutting, and H&E staining of frozen section slides with adequate level of competence such that if a histotechnologist was not available for frozen section (eg. at a future institution where the resident is completing his/her fellowship), the resident would be able to perform the frozen section independently.
  • In the grossing lab, the PGY1 resident will observe the pathology assistants at the opening bench primarily and learn the following: orientation, margin identification, margin sampling, tumour/specimen exposure to formalin and selecting scout sections if appropriate (EPA: TTD#1, C#1).
    • The PGY1 resident may also observe the pathologist assistant and senior residents grossing large specimens and, depending on skill acquisition, may attempt to gross simple/routine specimens (EPA: C#2).
    • Understand the difference between en face and perpendicular margins and embed them appropriately.
  • 2 days of cytology will be spent primarily with the cytotechs for onsite evaluation and learning about types of specimens/procedures and fixatives (EPA: C#11A).
  • 3 days in the histology and immunohistochemistry lab to learn basic principles of tissue processing:
    • Describe the steps through which tissue progresses from the gross room through to the pathologist's desk (processing, embedding, cutting, staining, etc.).
    • In a stepwise fashion, describe the procedures in the performance of the following ancillary diagnostic techniques (EPA: C#1):
      • Immunohistochemistry
      • Special histochemical stains
    • Understand the qualities of different tissue types and how they vary in the processing and cutting (eg. Fatty vs. fibrous vs. bone)
    • Understand the principles of choosing control tissues for immunohistochemistry
    • Describe the difference between on-slide and batch controls
  • Demonstrate the basic functioning of a microscope (TTD#3).
  • Demonstrate an understanding of a valid medical autopsy consent (EPA: C#6)
  • Demonstrate an understanding of the differences between a coroner (forensic) autopsy and a medical (hospital) autopsy (EPA: C#6, C#7).


Communicator Role

  • Understand rush specimens and how to handle these specimens in the gross room
  • Independently learn about surgical pathology critical values and the need to report these to the appropriate person
  • Be able to communicate with OR personnel (surgeons, OR nurses, residents and fellows) with respect to intra-operative consultation (frozen section) results and also to clarify the indication/need of the frozen section
  • Demonstrate and understanding of the need for on-site evaluation for cytology specimens
  • Demonstrate awareness of the importance of timeliness, clarity and accuracy in all verbal and written communications
  • Problem solve an incomplete/invalid hospital consent (EPA: C#6)

Collaborator Role

  • Shadow and assist a PGY2-5 resident as they prepare multidisciplinary rounds (MDR). Attend an MDR each week with a PGY2-5 resident or staff pathologist
  • Consult effectively with other physicians and health care professionals
  • Contribute effectively to interdisciplinary team activities
  • Understand the importance of contributing to educational/or research endeavors of clinical and laboratory colleagues
  • Be aware of the strong interface between the laboratory and clinical disciplines
  • Describe the role of Pathologist Assistants within the healthcare team
  • Describe the role of histotechnologists within the healthcare team
  • Describe the role of the cytotechnologists within the healthcare team
  • Describe the role of the morgue technologists within the healthcare team
  • Recognize the unique knowledge of and work collaboratively with histotechnologists and other laboratory personnel

Scholar Role

  • Explain the principles of evidence-based medicine and its relevance to clinical decision making
  • Record personal learning objectives during the rotation and take responsibility for self-managing your own learning objectives documental at the beginning of the rotation
  • Through reading and self-study, develop a basic understanding of and role of the following immunohistochemical and histochemical stains:
    • Immunohistochemistry:
      • Cytokeratins, in particular CK7 and CK20
      • CD45, CD3, CD20, CD68/CD163, CD138
      • S100
      • Approach to an undifferentiated tumour
      • Approach to carcinoma of unknown primary
    • Histochemical stains:
      • Special stains for microorganisms
      • Stains for pigment: hemosiderin, melanin
      • Special stains for tissue elements (Ie. Masson Trichroma, etc)
  • Seek ongoing feedback from teachers and modify learning objectives as necessary

Leader Role

  • Understand principles of quality assurance and patient safety
  • Allocate finite health care resources wisely
  • Utilize information technology to optimize patient care, life-long learning and other activities
  • Work effectively and efficiently in a health care organization

Professional Role

  • Demonstrate attention to laboratory safety:
    • Take universal precautionary measures to minimize hazardous exposures including potential infectious and chemical agents
    • Use personal protective measures (lab coats, goggles, gloves, etc.) as appropriate
  • Deliver highest quality care with integrity, honesty and compassion
  • Exhibit appropriate personal and interpersonal professional behaviours
  • Practice medicine ethically consistent with obligations of a physician
  • Adhere to hospital rules and accepted standards of dress while working
  • Demonstrate the knowledge, skills and attitudes relating to gender, culture, and ethnicity pertinent to anatomical pathology
  • Show up on time and attend all appropriate learning sessions and rounds
  • Complete all necessary evaluations on time


Rotation Checklist:




Grossing and processing:

  • Specimen identifiers and QA practices
  • Block selection for rush cases, biopsies, subspecialties, etc
  • Orientation and opening
  • Inking
  • Margin identification and sampling (en face vs perpendicular):
  • Fixation: type of fixative, ischemic type, size of sample and duration of fixation, tumour exposure to fixative
  • Symbols for histology on blocks (ie. “O” for lumen, # for pieces in cassette, etc)


Paraffin sectioning

  • Sectioning – different thickness
  • Angle blocks, always same orientation on slide
  • Localization of structures



  • Theory and protocol
  • Equipment
  • Antibody selection and titration
  • Ischemic time and impact on IHC stains
  • Overfixation and impact on IHC stains (rationale for scout section)
  • Decalcification and impact on IHC stains
  • Evaluating tissue controls on slide and ensuring appropriate
  • Troubleshooting (slide analysis)
  • Common artifacts


Histochemical (Special) Stains:

  • Examples of staining and application
  • Hands on training (Masson Trichrome, LFB)
  • Principles of the staining
  • Solutions (reuse, fresh, stock, etc.)
  • Differentiation
  • Controls and troubleshooting (examples of past issues)


Frozen Section:

  • Freeze fresh tissues (with and without isopentane)
  • Cryoprotection of fixed samples
  • Safety
  • Sectioning, temperature depending on type of samples
  • Staining (H&E)
  • Comparison of sections, identification of artifacts


Autopsy Suite:

  • Components of a valid autopsy consent
  • Types of autopsy: partial and full
  • Compare Forensic (Medicolegal) and Hospital (Medical) autopsy process
  • Safety practices in the morgue
  • Indications for neuropathology and/or cardiovascular pathology consultation



  • Types of cytopathology specimens
  • Role of the cytotechnologist (ie. Independent reporting, screening)
  • Adequacy in cytology specimens
  • Purpose of on-site evaluations
  • Types of fixatives


Updated April, 2022

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