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.

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 wsi_x.y.z.deb file and then run:

sudo apt install ./wsi_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.

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 <wsiFile> --outFolder <folder for generated files> --seriesDescription <text description>

Test data is freely available from OpenSlide.

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

If you're using Ubuntu, run the following command to download the dependencies and build the tool:

sudo ./cloud_build/ubuntuBuild.sh

Otherwise, follow these steps:

1. Download the source from the Releases tab or check out the repo.
2. Make sure that you have the following dependencies installed:

• g++ >=8
• cmake >=3
• boost >=1.69: https://www.boost.org/users/history/version_1_69_0.html
• dcmtk source ==3.6.2: https://dicom.offis.de/download/dcmtk/dcmtk362/dcmtk-3.6.2.zip
• openslide >=3.4.1
• libjpeg >= 8
• openjpeg >= 2.3.0
• jsoncpp >= 1.8.0

3. Run the following commands:

mkdir build
cd build
cp -R %dcmtkDir% ./dcmtk-3.6.2 
cmake ..
make -j%threads%