oracular (1) OrthancWSIDicomizer.1.gz

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 (=1)
              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
              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 © 2021-2023 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.