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https://github.com/GoogleCloudPlatform/wsi-to-dicom-converter
Conversion tool/library for converting whole slide images to DICOM
https://github.com/GoogleCloudPlatform/wsi-to-dicom-converter
dicom openslide wsi
Last synced: 9 days ago
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Conversion tool/library for converting whole slide images to DICOM
- Host: GitHub
- URL: https://github.com/GoogleCloudPlatform/wsi-to-dicom-converter
- Owner: GoogleCloudPlatform
- License: apache-2.0
- Created: 2019-06-11T21:45:05.000Z (about 5 years ago)
- Default Branch: develop
- Last Pushed: 2024-01-30T07:00:23.000Z (5 months ago)
- Last Synced: 2024-01-30T08:24:08.446Z (5 months ago)
- Topics: dicom, openslide, wsi
- Language: C++
- Homepage:
- Size: 7.79 MB
- Stars: 63
- Watchers: 12
- Forks: 25
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Codeowners: CODEOWNERS
Lists
- awesome-dicom - wsi-to-dicom-converter - Convert whole slide images (WSIs) to DICOM. (Libraries / C++)
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](https://openslide.org), 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](#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](http://openslide.cs.cmu.edu/download/openslide-testdata/).
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 is exceeded new files is started.
eg: 3 files will be generated if batch is 10 and 30 frames in level
##### threads
Threads to consume during execution.
##### debug
Print debug messages: dimensions of levels, size of frames.
##### dropFirstRowAndColumn
Drop first row and column of the source image in order to workaround bug https://github.com/openslide/openslide/issues/268
## Compiling from source
If you're using Ubuntu, run the following command to download the dependencies and build the tool:
```shell
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 ==3.6.6: https://github.com/DCMTK/dcmtk/archive/refs/tags/DCMTK-3.6.6.zip
- openslide >=3.4.1
- libjpeg_turbo >= 2.1.2 https://github.com/libjpeg-turbo/libjpeg-turbo/archive/refs/tags/2.1.2.zip
- openjpeg >= 2.3.0
- jsoncpp >= 1.8.0
- OpenCV >= 4.5.4. https://github.com/opencv/opencv/archive/refs/tags/4.5.4.zip
- abseil >= 20211102.0 https://github.com/abseil/abseil-cpp/archive/refs/tags/20211102.0.zip
3. Run the following commands:
```shell
mkdir build
cd build
cp -R %dcmtkDir% ./dcmtk-3.6.6
cmake ..
make -j%threads%
```