OrthancWSIDicomizer

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 <[email protected]>

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.