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pydicom DICOM Toolkit

A safety-first guide and CLI toolkit for reading, writing, converting and de-identification-preflighting local DICOM data with pydicom 3.0.2.

Dev & CodingAdvanced★ 33,030⑂ 3,248AI score 9/10Last updated: Aug 9, 2026

What it does

  • Safe dataset reads: shows dcmread() patterns with stop_before_pixels, specific_tags and defer_size, and explicitly forbids print(ds), full JSON dumps or logging element values because DICOM metadata can carry PHI.
  • Transfer syntax & codec preflight: decodes Transfer Syntax UIDs and maps out pinned plugin combinations (pylibjpeg, pyjpegls, python-gdcm, Pillow) plus supply-chain advice on hash-verified, internally mirrored wheels.
  • Pixel data handling: frame-scoped decoding via pydicom.pixels, array shape semantics, the correct Modality LUT → VOI LUT order, MONOCHROME1 inversion and Palette Color LUTs.
  • Compression / encapsulation: notes that compress() and decompress() mutate Pixel Data and mint a new SOP Instance UID, plus encapsulate() and generate_frames() usage.
  • Bounded de-identification workflow: a nine-step PS3.15 Annex E–aligned process covering original preservation, recursive sequence actions, one-to-one UID replacement, date-shift policy, burned-in annotation review and secret handling for UID keys/maps.
  • Seven helper CLIs: aggregate metadata, technical inventory, codec inspector, frame/memory planner, single non-diagnostic frame render, pseudonymizer + audit, and UID map validator.

Who it's for

  • Researchers and data engineers preprocessing medical imaging datasets in Python
  • Developers building PACS or imaging pipelines who must pin codec dependencies
  • Privacy/IRB engineers designing pseudonymization and audit trails before data sharing
  • Teams migrating pydicom 2.x code to the 3.0 API

Example uses

  1. Dataset triage: "Summarize modality, image size and transfer syntax across authorized/" → run scripts/dicom_inventory.py authorized/ --recursive for an aggregate report with no per-patient values exposed.
  2. Fixing decode errors: a JPEG 2000 CT series fails to open, so transfer_syntax_inspector.py reveals which plugins are installed and which pinned package to add.
  3. Research pseudonymization: generate a project key, run anonymize_dicom.py --uid-key-file project.key --uid-scope export-v1, then deidentification_audit.py on the derivative before expert sign-off.

· · · Install guide · · ·

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/pydicom folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/pydicom/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/pydicom ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Copy the skill into Claude Code's skills folder: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/pydicom ~/.claude/skills/
  3. Create and activate a Python virtual environment (e.g. python3 -m venv .venv && source .venv/bin/activate). Python 3.10+ is required.
  4. Install the reviewed pinned release: uv pip install "pydicom==3.0.2" (or pip install "pydicom==3.0.2").
  5. For pixel arrays and rendering add numpy==2.5.1 and Pillow==12.3.0; for compressed syntaxes install only the plugins you actually need (pylibjpeg family, pyjpegls, or python-gdcm).
  6. Restart Claude Code and ask something like "use pydicom to inspect this DICOM folder" — the skill triggers automatically.
  7. Only point it at local data you are authorized to access, keep originals untouched, and never commit, sync or share the generated UID key files.
View source on GitHub ↗License: MIT