Orthanc, lightweight, RESTful DICOM server for healthcare and medical research.
Create a DICOM file from a digital pathology image.
Genericoptions:--help Display this help and exit
--version
Output version information and exit
--verbose
Be verbose in logs
--threads arg (=4)
Number of processing threads to be used
--force-openslide arg (=0)
Whether to force the use of OpenSlide on input TIFF-like files (Boolean)
--openslide arg
Path to the shared library of OpenSlide (not necessary if converting from standard hierarchical
TIFF)
Optionsforthesourceimage:--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")
--padding arg (=1)
Add padding to plain PNG/JPEG/TIFF images to align the width/height to multiples of this value,
which enables deep zoom with IIIF (1 means no padding)
OptionsifimportingfromCytomine:--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)
Optionstoconstructthepyramid:--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
Optionsforthetargetimage:--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
Descriptionoftheimagedvolume:--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/HTTPSclientconfigurationtoaccesstheOrthancRESTAPI:--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
Advancedoptions:--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)
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