Unit 1 – Computer Science Foundations for Clinicians

You probably did not go into medicine to argue with file servers, graphics cards, and VPNs. But if you care about digital pathology, sooner or later you end up doing exactly that.

Unit 1 is a clinician-first primer on how computers, files, storage, networks, and basic security behave in real digital pathology workflows. The goal is not to turn you into an engineer. The goal is to give you enough language and mental models to:

Notice when something is wrong,
Guess where the bottleneck really is, and
Have calm, high-signal conversations with IT, vendors, and informatics colleagues.

Examples and stories are taken from whole-slide imaging (WSI), tumor boards, and day-to-day clinical work.

What this study guide is about

This study guide distils the Unit 1 essential-knowledge packs into three chapters:

Chapter 1 – Workstations, files, and storage: how CPU, RAM, SSDs/GPUs fit together, why WSI files feel big, and the basics of backup versus sync versus archive.
Chapter 2 – Naming, privacy, and networks: storage tiers and capacity planning, PHI-safe naming/versioning, practical privacy and security habits, and network/VPN fundamentals.
Chapter 3 – PC components for digital pathology: how to pick or justify workstation parts for viewing, AI-assisted work, or heavier research loads.

Where it helps, we connect concepts to WSI pyramids (tiles and zoom levels) and to QuPath-style workflows, but no coding is required.

What you can expect from this study guide

Self-contained chapters you can read in short bursts.
No programming; just enough technical language to be useful.
Clinic-style stories: tumor board mornings, slow slides, mysterious freezes, and “where did that file go?” moments.
Concrete recipes and checklists (for example, how to rename a folder safely, how to test your network in two minutes, how to set up basic backup habits).
Security that feels doable: password managers, MFA, disk encryption, and phishing drills designed for real clinical life, not idealized labs.
PC components explained in plain language, with budget-conscious options for viewing-only, AI-assisted, and heavier research workstations.

Detailed display calibration (for example, diagnostic-grade QA and standards) is handled in the dedicated digital pathology study guides. Here we stay at the level of “comfortable, honest screens” and how they fit into the wider system.

Why this is important

When the basics are fuzzy, small technical issues spiral into big clinical headaches:

A workstation that “feels slow” because RAM is full or the GPU is idle,
A WSI that stutters at tumor board because it lives on a congested network share,
A “backup” that was actually just a sync folder, with deletions spreading to everyone,
Filenames that quietly leak PHI or break when they cross systems,
A stolen laptop that was never encrypted,
A VPN that doubles latency and makes your viewer unusable from home.

Getting these foundations right reduces avoidable downtime, protects patients, and makes digital pathology and computational pathology projects much easier to grow.

We also point clearly to the governing privacy frameworks so you know what world you are operating in. For example:

In the United States, HIPAA and its de-identification guidance for PHI.
In Québec, the Act respecting health and social services information (R-22.1), the Act respecting the protection of personal information in the private sector (P-39.1, modernized by Law 25), and the Act respecting Access to documents held by public bodies and the Protection of personal information (A-2.1). PIPEDA can still apply to certain cross-border commercial activities.

What you will be able to do

By the end of Unit 1, you should be able to:

Read sizes and speeds realistically – understand bits, bytes, GB vs GiB, and what numbers actually matter for WSIs.
Map symptoms to likely bottlenecks – decide whether “the workstation is slow” smells like CPU, RAM, storage, network latency, or GPU issues.
Choose and organize storage sanely – distinguish local SSD/NVMe from NAS/SAN, sync from true backup, and apply 3-2-1 in practice.
Set up clinic-grade naming and versioning – create filenames and folder structures that travel cleanly across Windows, macOS, and Linux without leaking PHI, and keep one clear source of truth.
Practice simple, effective privacy and security habits – recognize PHI/PII, use a password manager with MFA, turn on device encryption, and follow a short response playbook when something feels wrong.
Explain networks without fear – know when to pick Wi-Fi versus Ethernet, what latency and bandwidth mean for WSIs, what VPNs change, and how to run a few quick diagnostics before calling IT.
Spec or defend a workstation build – read and discuss PC components in plain language, choose between a viewing-only, AI-assisted, or heavier research workstation, and justify those choices to IT, procurement, or a PI.
Send one high-signal ticket to IT – describe problems with concrete facts (where the slide lives, how big it is, network type, rough timings, viewer and version) instead of “it feels slow,” which saves everyone time.

Chapters overview

Chapter 1 – Workstations, files, and storage → Read now
Workstation anatomy, CPU/RAM/SSD/GPU trade-offs, common pitfalls for WSI files and formats, and storage basics including backup versus sync versus archive. Covers Chapters 1–3 of the essential knowledge pack.

Chapter 2 – Naming, privacy, and networks → Read now
Storage tiers and capacity planning, PHI-safe naming and versioning habits, privacy/security fundamentals, and network/VPN basics with practical troubleshooting. Covers Chapters 3–6 of the essential knowledge pack.

Chapter 3 – Picking the PC components for a digital pathology lab
A guided tour of CPUs, RAM, storage (inside the PC and in the lab), GPUs, displays, networking, power, and cooling – with three concrete build profiles: viewing-only, viewer plus AI assistance, and heavier research workloads. The emphasis is on understanding trade-offs and being able to justify a build to your institution.

--- title: "Unit 1 – Computer Science Foundations for Clinicians" body-classes: cs101-hide-crumbs --- You probably did not go into medicine to argue with file servers, graphics cards, and VPNs. But if you care about digital pathology, sooner or later you end up doing exactly that. Unit 1 is a clinician-first primer on how computers, files, storage, networks, and basic security behave in real digital pathology workflows. The goal is not to turn you into an engineer. The goal is to give you enough language and mental models to: * Notice when something is wrong, * Guess where the bottleneck really is, and * Have calm, high-signal conversations with IT, vendors, and informatics colleagues. Examples and stories are taken from whole-slide imaging (WSI), tumor boards, and day-to-day clinical work. --- ## What this study guide is about This study guide distils the Unit 1 essential-knowledge packs into three chapters: * **Chapter 1** – Workstations, files, and storage: how CPU, RAM, SSDs/GPUs fit together, why WSI files feel big, and the basics of backup versus sync versus archive. * **Chapter 2** – Naming, privacy, and networks: storage tiers and capacity planning, PHI-safe naming/versioning, practical privacy and security habits, and network/VPN fundamentals. * **Chapter 3** – PC components for digital pathology: how to pick or justify workstation parts for viewing, AI-assisted work, or heavier research loads. Where it helps, we connect concepts to WSI pyramids (tiles and zoom levels) and to QuPath-style workflows, but **no coding is required**. --- ## What you can expect from this study guide * **Self-contained chapters** you can read in short bursts. * **No programming**; just enough technical language to be useful. * **Clinic-style stories**: tumor board mornings, slow slides, mysterious freezes, and “where did that file go?” moments. * **Concrete recipes and checklists** (for example, how to rename a folder safely, how to test your network in two minutes, how to set up basic backup habits). * **Security that feels doable**: password managers, MFA, disk encryption, and phishing drills designed for real clinical life, not idealized labs. * **PC components explained in plain language**, with budget-conscious options for viewing-only, AI-assisted, and heavier research workstations. Detailed display calibration (for example, diagnostic-grade QA and standards) is handled in the dedicated digital pathology study guides. Here we stay at the level of “comfortable, honest screens” and how they fit into the wider system. --- ## Why this is important When the basics are fuzzy, small technical issues spiral into big clinical headaches: * A workstation that “feels slow” because RAM is full or the GPU is idle, * A WSI that stutters at tumor board because it lives on a congested network share, * A “backup” that was actually just a sync folder, with deletions spreading to everyone, * Filenames that quietly leak PHI or break when they cross systems, * A stolen laptop that was never encrypted, * A VPN that doubles latency and makes your viewer unusable from home. Getting these foundations right reduces avoidable downtime, protects patients, and makes digital pathology and computational pathology projects much easier to grow. We also point clearly to the governing privacy frameworks so you know **what world you are operating in**. For example: * In the United States, HIPAA and its de-identification guidance for PHI. * In Québec, the Act respecting health and social services information (R-22.1), the Act respecting the protection of personal information in the private sector (P-39.1, modernized by Law 25), and the Act respecting Access to documents held by public bodies and the Protection of personal information (A-2.1). PIPEDA can still apply to certain cross-border commercial activities. --- ## What you will be able to do By the end of Unit 1, you should be able to: * **Read sizes and speeds realistically** – understand bits, bytes, GB vs GiB, and what numbers actually matter for WSIs. * **Map symptoms to likely bottlenecks** – decide whether “the workstation is slow” smells like CPU, RAM, storage, network latency, or GPU issues. * **Choose and organize storage sanely** – distinguish local SSD/NVMe from NAS/SAN, sync from true backup, and apply 3-2-1 in practice. * **Set up clinic-grade naming and versioning** – create filenames and folder structures that travel cleanly across Windows, macOS, and Linux without leaking PHI, and keep one clear source of truth. * **Practice simple, effective privacy and security habits** – recognize PHI/PII, use a password manager with MFA, turn on device encryption, and follow a short response playbook when something feels wrong. * **Explain networks without fear** – know when to pick Wi-Fi versus Ethernet, what latency and bandwidth mean for WSIs, what VPNs change, and how to run a few quick diagnostics before calling IT. * **Spec or defend a workstation build** – read and discuss PC components in plain language, choose between a viewing-only, AI-assisted, or heavier research workstation, and justify those choices to IT, procurement, or a PI. * **Send one high-signal ticket to IT** – describe problems with concrete facts (where the slide lives, how big it is, network type, rough timings, viewer and version) instead of “it feels slow,” which saves everyone time. --- ## Chapters overview **Chapter 1 – Workstations, files, and storage** → [Read now](cs101_part1.qmd) Workstation anatomy, CPU/RAM/SSD/GPU trade-offs, common pitfalls for WSI files and formats, and storage basics including backup versus sync versus archive. Covers Chapters 1–3 of the essential knowledge pack. **Chapter 2 – Naming, privacy, and networks** → [Read now](cs101_part2.qmd) Storage tiers and capacity planning, PHI-safe naming and versioning habits, privacy/security fundamentals, and network/VPN basics with practical troubleshooting. Covers Chapters 3–6 of the essential knowledge pack. **Chapter 3 – Picking the PC components for a digital pathology lab** A guided tour of CPUs, RAM, storage (inside the PC and in the lab), GPUs, displays, networking, power, and cooling – with three concrete build profiles: viewing-only, viewer plus AI assistance, and heavier research workloads. The emphasis is on understanding trade-offs and being able to justify a build to your institution.