Man pages sections > man1 > OrthancWSIDicomizer

OrthancWSIDicomizer - Whole-slide imaging support for Orthanc

ORTHANCWSIDICOMIZER(1) User Commands ORTHANCWSIDICOMIZER(1)

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 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)
--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
--username arg
Username for the target Orthanc server
--password arg
Password for the target Orthanc server

Description of the imaged volume:

--imaged-width arg (=15)
With 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)

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@gmail.com> Copyright © 2012-2016 Sebastien Jodogne, Medical Physics Department, University Hospital of Liege (Belgium)
 
Copyright © 2017 Osimis S.A. (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 2017 OrthancWSIDicomizer 0.4