Pathology Informatics Study Path

Author

Fernando

Learning in progress

I am an MD with a background in computer science, not a board-certified pathologist or computational pathologist.
Everything here is part of my personal learning project. Notes, exercises, and code should not be used for diagnosis, treatment, or clinical decision-making.
Errors are possible; please treat this material as a starting point for discussion, not authoritative guidance.

Program overview

This notebook now hosts the full text that powers path.histopath.ai. The placeholder scaffolding is gone; in its place are the complete outlines for:

Unit 1 – Computer Science Foundations for Clinicians
Unit 2 – From Glass to Gigabytes
DCP 602 – Practical WSI Workflows, QA, and QuPath

As before, case studies and portfolio artifacts stay on the Astro site (histopath.ai) so this Quarto book can stay focused on syllabi, module briefs, and reading lists.

How to use this site

Pick a course and skim its overview. Each one starts with objectives, tooling, module map, and deliverables.
Dive into modules inside that same chapter. Each module section spells out clinical motivation, technical explanation, workflows, and references.
Follow outbound links to the main site if you need the companion artifacts (projects, datasets, recorded demos).

Course catalog

Unit 1 – Computer Science Foundations for Clinicians

Focus: Give clinicians and pathology leaders a shared computing vocabulary before they touch Linux, Git, Python, or scanners.

Read the course → Open Unit 1
Overview headlines: bits vs bytes, character encodings, hardware anatomy, operating systems, filesystems, and hospital network basics framed with lab analogies.
Outcome: build a “digital workstation anatomy” portfolio piece plus a checklist for conversations with IT, vendors, or digital pathology teams.

Unit 2 – From Glass to Gigabytes

Focus: Walk from accessioned tissue to living WSIs, covering scanners, storage, metadata, standards, and operations math.

Read the course → Open Unit 2
Overview headlines: WSI internals, viewer/storage/network interplay, slide identity, standards (SNOMED CT, ICD-O, LOINC, DICOM), and long-term operations planning.
Outcome: produce a “WSI Pipeline Blueprint” with diagrams, explanations, and five-year capacity estimates for a hypothetical lab.

DCP 602 – Practical WSI Workflows, QA, and QuPath

Focus: Turn QuPath into a dependable digital microscope for QA, annotation, and classic image analysis—no scripting required.

Overview headlines: QuPath installation, project hygiene, ROI discipline, artifact logging, tissue/cell detection, biomarker quantification, and measurement export.
Outcome: craft a QuPath-based QA project with labeled ROIs, QC screenshots, exported tables, and a clinician-friendly README.

Future courses (DCP 611+, 62x, etc.) will reuse this same pattern once their drafts are ready.

Feedback welcome

If you spot mistakes or want to collaborate, email fsoto@histopath.ai. Each course outline carries TODO markers - feel free to annotate those first so I can iterate quickly.

--- title: "Pathology Informatics Learning Path" --- ::: {.callout-warning title="Learning in progress"} - I am an MD with a background in computer science, not a board-certified pathologist or computational pathologist. - Everything here is part of my personal learning project. Notes, exercises, and code should not be used for diagnosis, treatment, or clinical decision-making. - Errors are possible; please treat this material as a starting point for discussion, not authoritative guidance. ::: ## Program overview This notebook now hosts the full text that powers **path.histopath.ai**. The placeholder scaffolding is gone; in its place are the complete outlines for: - **Unit 1 – Computer Science Foundations for Clinicians** - **Unit 2 – From Glass to Gigabytes** - **DCP 602 – Practical WSI Workflows, QA, and QuPath** As before, case studies and portfolio artifacts stay on the Astro site (`histopath.ai`) so this Quarto book can stay focused on syllabi, module briefs, and reading lists. ## How to use this site 1. **Pick a course** and skim its overview. Each one starts with objectives, tooling, module map, and deliverables. 2. **Dive into modules** inside that same chapter. Each module section spells out clinical motivation, technical explanation, workflows, and references. 3. **Follow outbound links** to the main site if you need the companion artifacts (projects, datasets, recorded demos). ## Course catalog ::: {.callout-note title="Unit 1 – Computer Science Foundations for Clinicians"} **Focus:** Give clinicians and pathology leaders a shared computing vocabulary before they touch Linux, Git, Python, or scanners. - **Read the course** → [Open Unit 1](cs101/index.qmd) - **Overview headlines:** bits vs bytes, character encodings, hardware anatomy, operating systems, filesystems, and hospital network basics framed with lab analogies. - **Outcome:** build a “digital workstation anatomy” portfolio piece plus a checklist for conversations with IT, vendors, or digital pathology teams. ::: ::: {.callout-note title="Unit 2 – From Glass to Gigabytes"} **Focus:** Walk from accessioned tissue to living WSIs, covering scanners, storage, metadata, standards, and operations math. - **Read the course** → [Open Unit 2](dcp601/index.qmd) - **Overview headlines:** WSI internals, viewer/storage/network interplay, slide identity, standards (SNOMED CT, ICD-O, LOINC, DICOM), and long-term operations planning. - **Outcome:** produce a “WSI Pipeline Blueprint” with diagrams, explanations, and five-year capacity estimates for a hypothetical lab. ::: ::: {.callout-note title="DCP 602 – Practical WSI Workflows, QA, and QuPath"} **Focus:** Turn QuPath into a dependable digital microscope for QA, annotation, and classic image analysis—no scripting required. - **Overview headlines:** QuPath installation, project hygiene, ROI discipline, artifact logging, tissue/cell detection, biomarker quantification, and measurement export. - **Outcome:** craft a QuPath-based QA project with labeled ROIs, QC screenshots, exported tables, and a clinician-friendly README. ::: Future courses (DCP 611+, 62x, etc.) will reuse this same pattern once their drafts are ready. ## Feedback welcome If you spot mistakes or want to collaborate, email `fsoto@histopath.ai`. Each course outline carries TODO markers - feel free to annotate those first so I can iterate quickly.