wsi-to-dicom-converter

Source code on GitHub.

README

WSI to DICOM Converter

This repository contains a tool that converts whole slide images (WSIs) to DICOM. To read the underlying whole slide images (WSIs), this tool relies on OpenSlide, which supports a variety of file formats.

Quickstart

Debian-based Linux

To download the latest release, on the Releases tab, download the installer for your operating system and then run it. For example, if you're running on a Debian-based system, download the wsi2dcm_x.y.z.deb file and then run:

`` sudo apt install ./wsi2dcm_x.y.z.deb ` Note: if you get an error about missing shared libraries, run sudo ldconfig or make sure that /usr/local/lib is in your LD_LIBRARY_PATH.

You may also need to install the following packages and their dependencies with sudo apt-get install: * libtiff-dev * libxml2-dev * libcairo-dev * gtk2-engines-pixbuf

MacOS

` brew install wsi2dcm.rb `

If an installer isn't available for your operating system, see Compiling from source.

After you have installed the WSI to DICOM converter, to convert a file, run the following command:

` wsi2dcm --input --outFolder --seriesDescription `

Test data is freely available from OpenSlide.

To see all available options, run: wsi2dcm --help.

Complete set of parameters

##### input Input wsi file, supported by openslide. ##### outFolder Folder to store dcm files ##### tileHeight Tile height px. ##### tileWidth Tile width px. ##### levels Number of levels to generate, levels == 0 means number of levels will be read from wsi file. ##### downsamples Size factor for each level for each level, downsample is size factor for each level.

eg: if base level size is 100x100 and downsamples is (1, 2, 10) then

level0 100x100

level1 50x50

level2 10x10

##### startOn Level to start generation. ##### stopOn Level to stop generation. ##### sparse Use TILED_SPARSE frame organization, by default it's TILED_FULL http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.17.3.html ##### compression Compression, supported compressions: jpeg, jpeg2000, raw. ##### seriesDescription (0008,103E) [LO] SeriesDescription Dicom tag. ##### studyId (0020,000D) [UI] StudyInstanceUID Dicom tag. ##### seriesId (0020,000E) [UI] SeriesInstanceUID Dicom tag. ##### jsonFile Dicom json file with additional tags https://www.dicomstandard.org/dicomweb/dicom-json-format/ ##### batch Maximum frames in one file, as limit ...