ORTHANCWSIDICOMIZER(1)

📦
version 3.3 · 5 versions
, in ubuntu resolute, ubuntu stonking

✨ NAME ✨

Okay bestie, this is the User Commands page for ORTHANCWSIDICOMIZER(1) 💖 The tool is OrthancWSIDicomizer, and it gives whole-slide imaging support for Orthanc 🔬✨

🎀 SYNOPSIS 🎀

OrthancWSIDicomizer [OPTION]... [INPUT]

🦋 DESCRIPTION 🦋

So Orthanc is a lightweight, RESTful DICOM server made for healthcare and medical research 🏥 Iconic.

And this tool's whole thing? It creates a DICOM file from a digital pathology image 🧬 Main character energy, no cap.

💖 OPTIONS 💖

✨ Generic options ✨

  • --help — Shows this help and exits 🙈
  • --version — Prints the version info and exits 🧾
  • --verbose — Gets extra chatty in the logs 📣
  • --threads arg (default 4) — How many processing threads to use 🧵
  • --force-openslide arg (default 0) — Forces OpenSlide to be used on TIFF-like input files (Boolean) 🔥
  • --openslide arg — Path to the OpenSlide shared library (not needed if you're converting a standard hierarchical TIFF) 📚

🌸 Options for the source image 🌸

  • --dataset arg — Path to a JSON file holding the DICOM dataset 🗂️
  • --sample-dataset — Shows a minimalistic sample DICOM dataset in JSON format, then exits 🍓
  • --reencode arg — Whether to re-encode each tile (no transcoding, much slower) (Boolean) 🐢
  • --repaint arg — Whether to repaint the background of the image (Boolean) 🎨
  • --color arg — Color of the background, like "255,0,0" 🌈
  • --padding arg (default 1) — Adds padding to plain PNG/JPEG/TIFF images so the width and height line up with multiples of this value, which enables deep zoom with IIIF (1 means no padding) 🧩

🧚 Options if importing from Cytomine 🧚

  • --cytomine-url arg — URL of the source Cytomine server, for instance https://demo.cytomine.be/ 🔗
  • --cytomine-public-key arg — Your personal public key in Cytomine (check Account in the Cytomine Web interface) 🔑
  • --cytomine-private-key arg — Your personal private key. Keep it SECRET, bestie 🤫
  • --cytomine-image arg — ID of the Image Instance you want in Cytomine (must be an integer) 🖼️
  • --cytomine-compression arg (default jpeg) — Compression used to download tiles from Cytomine: "jpeg" (faster) or "png" (better quality) 💜

🫶 Options to construct the pyramid 🫶

  • --pyramid arg (default 0) — Rebuilds the full pyramid (slow) (Boolean) 🐌
  • --smooth arg (default 0) — Applies smoothing when rebuilding the pyramid (slower, but higher quality) (Boolean) ✨
  • --levels arg — Number of levels in the target pyramid 🪜

👑 Options for the target image 👑

  • --tile-width arg — Width of the tiles in the target image 📐
  • --tile-height arg — Height of the tiles in the target image 📏
  • --compression arg — Compression for the target image: "none", "jpeg", "jpeg2000", or "jpeg-ls" 🗜️
  • --jpeg-quality arg — Quality level for JPEG, from 0..100 💎
  • --max-size arg (default 10) — Max size per DICOM instance, in MB. 0 means no limit on the file size 📦
  • --folder arg — Folder where the output DICOM instances get stored 📁
  • --folder-pattern arg (default wsi-%06d.dcm) — Naming pattern for the files in the output folder 🏷️
  • --encoding arg (default Latin1) — The character set used in the generated DICOM instances. Allowed values are: "Ascii", "Utf8", "Latin1", "Latin2", "Latin3", "Latin4", "Latin5", "Cyrillic", "Windows1251", "Arabic", "Greek", "Hebrew", "Thai", "Japanese", "Chinese", "Korean", "JapaneseKanji", and "SimplifiedChinese" 🌏
  • --orthanc arg (default http://localhost:8042/) — URL to the REST API of the target Orthanc server 🛰️

🌷 Description of the imaged volume 🌷

  • --imaged-width arg — Width of the specimen (in mm), in the coordinate system of the glass slide. Defaults to 15mm if missing 📏
  • --imaged-height arg — Height of the specimen (in mm), in the coordinate system of the glass slide. Defaults to 15mm if missing 📏
  • --imaged-depth arg (default 1) — Depth of the specimen (in mm) 🫧
  • --offset-x arg (default 20) — X offset of the specimen, relative to the slide coordinates origin (in mm) ➡️
  • --offset-y arg (default 40) — Y offset of the specimen, relative to the slide coordinates origin (in mm) ⬆️

🌐 HTTP/HTTPS client configuration to access the Orthanc REST API 🌐

  • --username arg — Username for the target Orthanc server 🙋
  • --password arg — Password for the target Orthanc server 🔐
  • --proxy arg — HTTP proxy to use 🚪
  • --timeout arg (default 0) — HTTP timeout in seconds. 0 means no timeout ⏳
  • --verify-peers arg (default 1) — Turns on peer verification during HTTPS requests 🛡️
  • --ca-certificates arg — Path to the CA (certification authority) certificates used to validate peers in HTTPS requests 📜

🔮 Advanced options 🔮

  • --optical-path arg (default brightfield) — Optical path automatically added to the DICOM dataset ("none" or "brightfield") 🔦
  • --icc-profile arg — Path to the ICC profile to include. If empty, a default sRGB profile gets added 🎨
  • --safety arg (default 1) — Runs extra checks to verify the source image is supported (might slow things down) (Boolean) 🧐
  • --lower-levels arg — Number of pyramid levels up to which multithreading should be applied (only for performance/memory tuning) ⚙️

🫶 AUTHOR 🫶

Written by Sebastien Jodogne <s.jodogne@orthanc-labs.com> 💌

  • Copyright © 2012-2016 Sebastien Jodogne, Medical Physics Department, University Hospital of Liege (Belgium) 🏛️
  • Copyright © 2017-2023 Osimis S.A. (Belgium) 🏢
  • Copyright © 2024-2025 Orthanc Team SRL (Belgium) 🤝
  • Copyright © 2021-2025 Sebastien Jodogne, ICTEAM UCLouvain (Belgium) 🎓
  • Licensing AGPL: GNU AGPL version 3 or later <http://gnu.org/licenses/agpl.html>. 📜
  • This is free software: you are free to change and redistribute it. 🦋
  • There is NO WARRANTY, to the extent permitted by law. 🙈

Version 3.3, November 2025 — stay iconic, bestie 💖🦋✨

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