A command for cutting whole-slide images into smaller image tiles after locating the tissue. Whole-slide images are very large microscope scans, often stored as SVS, NDPI, or MRXS files.

Use it to prepare pathology slides for machine-learning models, choose a target microns-per-pixel resolution, remove mostly empty tiles, and record slide and tissue details.

It keeps tile locations and physical image scale correct across scanners, avoiding patches from the wrong region or models that learn scanner differences instead of tissue patterns.

tile-wsi — Command for Claude Code by zamushwani/biomedical-ai-skills

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Clone the repo

git clone --depth 1 https://github.com/zamushwani/biomedical-ai-skills

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/tile-wsi/github.svg)](https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/tile-wsi)

Your own site

<a href="https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/tile-wsi"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/tile-wsi/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/tile-wsi"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/tile-wsi.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 0 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.

When invoked 420 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00000	$0.00420
Opus 5.5	$0.00000	$0.00168
Sonnet 5.5	$0.00000	$0.00084
Haiku 4.5	$0.00000	$0.00042

Measured 2mo ago against content hash e68c8980786f, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

tile-wsi scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude/commands/tile-wsi.md · 24 lines

What it actually says

Tile the slide at $0 at a target resolution of $1 microns per pixel (default: 0.5).

Follow the computational-pathology skill. Two bugs cost the most time here:

read_region(location, level, size) mixes coordinate frames. location is in the level 0 frame; size is in the target level frame. Scale the location by level_downsamples[level]. The failure is silent: correct shape, wrong region — and a level-0 prototype hides it entirely.
Magnification is not resolution. "40x" maps to roughly 0.23–0.28 um/px depending on scanner, so tiles cut at "40x" from two scanners sit at different physical scales and the model learns the scanner. Work in mpp.

Also:

level_downsamples are floats (4.000122, not 4). Pick levels with get_best_level_for_downsample, never ==.
Composite RGBA onto white. .convert("RGB") composites onto black, turning unscanned area into dark tissue-coloured pixels.
Detect tissue by saturation, not intensity — glass is bright and unsaturated, while pale adipose is real signal.
Record the tissue-fraction threshold. ">50% tissue" and ">10% tissue" are different datasets.

Report: slide mpp and vendor, level chosen, tile count, tissue fraction threshold, and tile coordinates in the level 0 frame.

If $0 is empty, ask for the slide path.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2mo ago First seen · 24 lines · 0 tokens per session scan A e68c8980786f

Subscribe to this mod's changes

tile-wsi is a command published in the GitHub repository zamushwani/biomedical-ai-skills (1 stars, last pushed 1mo ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 420 tokens. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

DESeq2 Scientific ai-agent ai-skills bioinformatics cancer-genomics cancer-research

tile-wsi next to 6 commands from other repositories
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tile-wsizamushwani/biomedical-ai-skills	Command	1	1mo ago	MIT	A	0	Claude Code
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