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 (=2): Number of processing threads to be used
--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")

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" or "jpeg2000")
--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 (=15): Width of the specimen (in mm)
--imaged-height arg (=15): Height of the specimen (in mm)
--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 © 2017-2021 Osimis S.A. (Belgium)
Copyright © 2021-2021 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.

March 2022

OrthancWSIDicomizer 1.1