---
name: "OrthancWSIDicomizer"
section: "1"
platform: "linux"
package: "orthanc-wsi"
version: "3.2+dfsg-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/OrthancWSIDicomizer"
---

# OrthancWSIDicomizer(1)

Whole-slide imaging support for Orthanc

## NAME

OrthancWSIDicomizer - Whole-slide imaging support for Orthanc

## SYNOPSIS

**OrthancWSIDicomizer** \[*OPTION*\]... \[*INPUT*\]

## DESCRIPTION

Orthanc, lightweight, RESTful DICOM server for healthcare and medical research.

Create a DICOM file from a digital pathology image.

### Generic options:

- **--help**

  Display this help and exit

- **--version**

  Output version information and exit

- **--verbose**

  Be verbose in logs

- **--threads** arg (=4)

  Number of processing threads to be used

- **--force-openslide** arg (=0)

  Whether to force the use of OpenSlide on input TIFF-like files (Boolean)

- **--openslide** arg

  Path to the shared library of OpenSlide (not necessary if converting from standard hierarchical TIFF)

### Options for the source image:

- **--dataset** arg

  Path to a JSON file containing the DICOM dataset

- **--sample-dataset**

  Display a minimalistic sample DICOM dataset in JSON format, then exit

- **--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 (e.g. "255,0,0")

- **--padding** arg (=1)

  Add padding to plain PNG/JPEG/TIFF images to align the width/height to 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 (cf. Account in the Cytomine Web interface)

- **--cytomine-private-key** arg

  Your personal private key in Cytomine (to be kept secret)

- **--cytomine-image** arg

  ID of the Image Instance of interest in Cytomine (must be an integer)

- **--cytomine-compression** arg (=jpeg)

  Compression to be used for downloading the tiles from Cytomine, can be "jpeg" (faster) or "png" (better quality)

### Options to construct the pyramid:

- **--pyramid** arg (=0)

  Reconstruct the full pyramid (slow) (Boolean)

- **--smooth** arg (=0)

  Apply smoothing when reconstructing 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 of the target image ("none", "jpeg", "jpeg2000", or "jpeg-ls")

- **--jpeg-quality** arg

  Set quality level for JPEG (0..100)

- **--max-size** arg (=10)

  Maximum size per DICOM instance (in MB), 0 means no limit on the file size

- **--folder** arg

  Folder where to store the output DICOM instances

- **--folder-pattern** arg (=wsi-%06d.dcm)

  Pattern for the files in the output folder

- **--orthanc** arg (=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 (=1)

  Depth of the specimen (in mm)

- **--offset-x** arg (=20)

  X offset the specimen, wrt. slide coordinates origin (in mm)

- **--offset-y** arg (=40)

  Y offset the specimen, wrt. 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 be used

- **--timeout** arg (=0)

  HTTP timeout (in seconds, 0 means no timeout)

- **--verify-peers** arg (=1)

  Enable the verification of the peers during HTTPS requests

- **--ca-certificates** arg

  Path to the CA (certification authority) certificates to validate peers in HTTPS requests

### Advanced options:

- **--optical-path** arg (=brightfield)

  Optical path to be automatically added to the DICOM dataset ("none" or "brightfield")

- **--icc-profile** arg

  Path to the ICC profile to be included. If empty, a default sRGB profile will be added.

- **--safety** arg (=1)

  Whether to do additional checks to verify the source image is supported (might slow 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

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.