.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.1.
.TH ORTHANCWSIDICOMIZER "1" "March 2022" "OrthancWSIDicomizer 1.1" "User Commands"
.SH NAME
OrthancWSIDicomizer \- Whole-slide imaging support for Orthanc
.SH SYNOPSIS
.B OrthancWSIDicomizer
[\fI\,OPTION\/\fR]... [\fI\,INPUT\/\fR]
.SH DESCRIPTION
Orthanc, lightweight, RESTful DICOM server for healthcare and medical research.
.PP
Create a DICOM file from a digital pathology image.
.SS "Generic options:"
.TP
\fB\-\-help\fR
Display this help and exit
.TP
\fB\-\-version\fR
Output version information and exit
.TP
\fB\-\-verbose\fR
Be verbose in logs
.TP
\fB\-\-threads\fR arg (=2)
Number of processing threads to be used
.TP
\fB\-\-openslide\fR arg
Path to the shared library of OpenSlide
(not necessary if converting from
standard hierarchical TIFF)
.SS "Options for the source image:"
.TP
\fB\-\-dataset\fR arg
Path to a JSON file containing the
DICOM dataset
.TP
\fB\-\-sample\-dataset\fR
Display a minimalistic sample DICOM
dataset in JSON format, then exit
.TP
\fB\-\-reencode\fR arg
Whether to re\-encode each tile (no
transcoding, much slower) (Boolean)
.TP
\fB\-\-repaint\fR arg
Whether to repaint the background of
the image (Boolean)
.TP
\fB\-\-color\fR arg
Color of the background (e.g.
"255,0,0")
.SS "Options if importing from Cytomine:"
.TP
\fB\-\-cytomine\-url\fR arg
URL of the source Cytomine server, for
instance: https://demo.cytomine.be/
.TP
\fB\-\-cytomine\-public\-key\fR arg
Your personal public key in Cytomine
(cf. Account in the Cytomine Web
interface)
.TP
\fB\-\-cytomine\-private\-key\fR arg
Your personal private key in Cytomine
(to be kept secret)
.TP
\fB\-\-cytomine\-image\fR arg
ID of the Image Instance of interest in
Cytomine (must be an integer)
.TP
\fB\-\-cytomine\-compression\fR arg (=jpeg)
Compression to be used for downloading
the tiles from Cytomine, can be "jpeg"
(faster) or "png" (better quality)
.SS "Options to construct the pyramid:"
.TP
\fB\-\-pyramid\fR arg (=0)
Reconstruct the full pyramid (slow)
(Boolean)
.TP
\fB\-\-smooth\fR arg (=0)
Apply smoothing when reconstructing the
pyramid (slower, but higher quality)
(Boolean)
.TP
\fB\-\-levels\fR arg
Number of levels in the target pyramid
.SS "Options for the target image:"
.TP
\fB\-\-tile\-width\fR arg
Width of the tiles in the target image
.TP
\fB\-\-tile\-height\fR arg
Height of the tiles in the target image
.TP
\fB\-\-compression\fR arg
Compression of the target image
("none", "jpeg" or "jpeg2000")
.TP
\fB\-\-jpeg\-quality\fR arg
Set quality level for JPEG (0..100)
.TP
\fB\-\-max\-size\fR arg (=10)
Maximum size per DICOM instance (in
MB), 0 means no limit on the file size
.TP
\fB\-\-folder\fR arg
Folder where to store the output DICOM
instances
.TP
\fB\-\-folder\-pattern\fR arg (=wsi\-%06d.dcm)
Pattern for the files in the output
folder
.TP
\fB\-\-orthanc\fR arg (=http://localhost:8042/)
URL to the REST API of the target
Orthanc server
.SS "Description of the imaged volume:"
.TP
\fB\-\-imaged\-width\fR arg (=15)
Width of the specimen (in mm)
.TP
\fB\-\-imaged\-height\fR arg (=15)
Height of the specimen (in mm)
.TP
\fB\-\-imaged\-depth\fR arg (=1)
Depth of the specimen (in mm)
.TP
\fB\-\-offset\-x\fR arg (=20)
X offset the specimen, wrt. slide
coordinates origin (in mm)
.TP
\fB\-\-offset\-y\fR arg (=40)
Y offset the specimen, wrt. slide
coordinates origin (in mm)
.SS "HTTP/HTTPS client configuration to access the Orthanc REST API:"
.TP
\fB\-\-username\fR arg
Username for the target Orthanc server
.TP
\fB\-\-password\fR arg
Password for the target Orthanc server
.TP
\fB\-\-proxy\fR arg
HTTP proxy to be used
.TP
\fB\-\-timeout\fR arg (=0)
HTTP timeout (in seconds, 0 means no
timeout)
.TP
\fB\-\-verify\-peers\fR arg (=1)
Enable the verification of the peers
during HTTPS requests
.TP
\fB\-\-ca\-certificates\fR arg
Path to the CA (certification
authority) certificates to validate
peers in HTTPS requests
.SS "Advanced options:"
.TP
\fB\-\-optical\-path\fR arg (=brightfield)
Optical path to be automatically added
to the DICOM dataset ("none" or
"brightfield")
.TP
\fB\-\-icc\-profile\fR arg
Path to the ICC profile to be included.
If empty, a default sRGB profile will
be added.
.TP
\fB\-\-safety\fR arg (=1)
Whether to do additional checks to
verify the source image is supported
(might slow down) (Boolean)
.TP
\fB\-\-lower\-levels\fR arg
Number of pyramid levels up to which
multithreading should be applied (only
for performance/memory tuning)
.SH AUTHOR
Written by Sebastien Jodogne <s.jodogne@orthanc\-labs.com>
.SH COPYRIGHT
Copyright \(co 2012\-2016 Sebastien Jodogne, Medical Physics Department, University Hospital of Liege (Belgium)
.br
Copyright \(co 2017\-2021 Osimis S.A. (Belgium)
.br
Copyright \(co 2021\-2021 Sebastien Jodogne, ICTEAM UCLouvain (Belgium)
Licensing AGPL: GNU AGPL version 3 or later <http://gnu.org/licenses/agpl.html>.
.br
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.