table of contents
| 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), 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) 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.
| January 2021 | OrthancWSIDicomizer 1.0 |