Anatomic Pathology Workflow: Accessioning to Sign-Out

An anatomic pathology case moves through more discrete, physically-handled stages than almost any other lab workflow — the specimen itself changes form at nearly every step. Understanding where each stage hands off to the next is the difference between a workflow that self-reports its own bottlenecks and one where a stalled case just quietly sits.

1. Accessioning

The specimen arrives with a requisition, gets logged, assigned a unique case number, and matched to patient demographics, ordering provider, and clinical history. This is also where specimen integrity gets its first check — correct container, adequate fixation, labeling matches the requisition.

Where it stalls: mismatched or incomplete requisition data, forcing a hold-and-clarify loop with the ordering provider before the case can proceed.

2. Grossing

A pathologist or pathologists' assistant examines the specimen grossly, describes it, and selects representative sections for processing. This stage produces the gross description that becomes part of the final report, and determines exactly which tissue sections move forward.

Where it stalls: grossing volume backing up behind a single pathologist or PA, especially for complex specimens requiring extensive sectioning.

3. Processing

Tissue sections are dehydrated, cleared, and infiltrated with paraffin — typically overnight, on a fixed processor cycle. This stage is largely automated but time-locked; a specimen that misses the processor's start time loses a full cycle.

4. Embedding

Processed tissue sections are oriented and embedded in paraffin blocks. Correct orientation here directly determines whether the eventual slide shows the diagnostically relevant plane of tissue — a rework at this stage means a full processing cycle wasted.

5. Cutting (microtomy)

Thin sections are cut from the paraffin block and mounted on slides. This is a skill-dependent, manual step where technique directly affects slide quality — a poorly cut section can force a re-cut and can, in tissue-limited cases, exhaust the available block.

6. Staining

Slides are stained — routinely H&E, with special stains or immunohistochemistry (IHC) added when the case requires additional diagnostic information. Staining protocols are highly standardized but instrument- and reagent-lot dependent, which ties this stage back into the lab's broader QC program.

Where it stalls: IHC requests that come back after initial H&E review, effectively restarting part of the workflow on the same case.

7. Pathologist review and diagnosis

The pathologist reviews slides against the gross description and clinical history, arrives at a diagnosis, and may request additional stains, sections, or a consult before finalizing.

Where it stalls: consult requests to a subspecialist pathologist, which can add days depending on availability — a common and legitimate source of TAT variability that still needs to be tracked, not just excused.

8. Report generation and sign-out

The final report is compiled — gross description, microscopic findings, diagnosis, and any synoptic reporting elements required for the specimen type (particularly for oncology cases, where structured synoptic data feeds staging and treatment decisions). The pathologist signs out the case, which releases the report to the ordering provider.

Where TAT actually gets lost

Across these eight stages, the two most common sources of unexplained turnaround time are the same across most labs: specimens waiting between stages rather than being actively worked (a case grossed on Monday but not embedded until Wednesday because it sat in a batch queue), and rework triggered late — an IHC order added after initial review, a re-cut needed because the first section wasn't diagnostic. Neither of these shows up if the only thing tracked is "received to resulted" as a single number.

What a workflow system should actually show

Real visibility into an anatomic pathology workflow means tracking each case's time in each stage, not just start and end — so a lab can see whether a TAT problem is concentrated in grossing backlog, processor scheduling, cutting rework, or pathologist queue depth, and fix the actual bottleneck instead of generically "working faster" everywhere.