{"id":15222146,"url":"https://github.com/googlecloudplatform/wsi-to-dicom-converter","last_synced_at":"2025-04-09T16:03:31.801Z","repository":{"id":38328149,"uuid":"191454643","full_name":"GoogleCloudPlatform/wsi-to-dicom-converter","owner":"GoogleCloudPlatform","description":"Conversion tool/library for converting whole slide images to DICOM","archived":false,"fork":false,"pushed_at":"2024-05-01T17:28:29.000Z","size":8168,"stargazers_count":79,"open_issues_count":11,"forks_count":27,"subscribers_count":24,"default_branch":"develop","last_synced_at":"2024-12-18T08:41:33.091Z","etag":null,"topics":["dicom","openslide","wsi"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/GoogleCloudPlatform.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":"CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-06-11T21:45:05.000Z","updated_at":"2024-12-06T08:36:56.000Z","dependencies_parsed_at":"2023-01-29T01:30:13.637Z","dependency_job_id":"bd2d1320-43f0-4c28-9aef-5e6958ac028d","html_url":"https://github.com/GoogleCloudPlatform/wsi-to-dicom-converter","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GoogleCloudPlatform%2Fwsi-to-dicom-converter","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GoogleCloudPlatform%2Fwsi-to-dicom-converter/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GoogleCloudPlatform%2Fwsi-to-dicom-converter/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GoogleCloudPlatform%2Fwsi-to-dicom-converter/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/GoogleCloudPlatform","download_url":"https://codeload.github.com/GoogleCloudPlatform/wsi-to-dicom-converter/tar.gz/refs/heads/develop","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":237243005,"owners_count":19278060,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["dicom","openslide","wsi"],"created_at":"2024-09-28T15:10:48.554Z","updated_at":"2025-02-05T04:31:58.984Z","avatar_url":"https://github.com/GoogleCloudPlatform.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# WSI to DICOM Converter\n\nThis 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.\n\n## Quickstart\n\n### Debian-based Linux\nTo 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:\n\n```\nsudo apt install ./wsi2dcm_x.y.z.deb\n```\nNote: 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`.\n\nYou may also need to install the following packages and their dependencies with `sudo apt-get install`:\n* `libtiff-dev`\n* `libxml2-dev`\n* `libcairo-dev`\n* `gtk2-engines-pixbuf`\n\n### MacOS\n\n```\nbrew install wsi2dcm.rb\n```\n\n\nIf an installer isn't available for your operating system, see [Compiling from source](#compiling-from-source).\n\nAfter you have installed the WSI to DICOM converter, to convert a file, run the following command:\n\n```\nwsi2dcm --input \u003cwsiFile\u003e --outFolder \u003cfolder for generated files\u003e --seriesDescription \u003ctext description\u003e\n```\n\nTest data is freely available from [OpenSlide](http://openslide.cs.cmu.edu/download/openslide-testdata/).\n\nTo see all available options, run: `wsi2dcm --help`.\n\n## Complete set of parameters\n\n##### input\nInput wsi file, supported by openslide.\n##### outFolder\nFolder to store dcm files\n##### tileHeight\nTile height px.\n##### tileWidth\nTile width px.\n##### levels\nNumber of levels to generate, levels == 0 means number of levels will be read from wsi file.\n##### downsamples\nSize factor for each level  for each level, downsample is size factor for each level.\n\neg: if base level size is 100x100 and downsamples is (1, 2, 10) then\n- level0 100x100\n- level1 50x50\n- level2 10x10\n##### startOn\nLevel to start generation.\n##### stopOn\nLevel to stop generation.\n##### sparse\nUse 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\n##### compression\nCompression, supported compressions: jpeg, jpeg2000, raw.\n##### seriesDescription\n(0008,103E) [LO] SeriesDescription Dicom tag.\n##### studyId\n(0020,000D) [UI] StudyInstanceUID Dicom tag.\n##### seriesId\n(0020,000E) [UI] SeriesInstanceUID Dicom tag.\n##### jsonFile\nDicom json file with additional tags https://www.dicomstandard.org/dicomweb/dicom-json-format/\n##### batch\nMaximum frames in one file, as limit is exceeded new files is started.\n\neg: 3 files will be generated if batch is 10 and 30 frames in level\n##### threads\nThreads to consume during execution.\n##### debug\nPrint debug messages: dimensions of levels, size of frames.\n##### dropFirstRowAndColumn\nDrop first row and column of the source image in order to workaround bug https://github.com/openslide/openslide/issues/268\n\n## Compiling from source\n\nUsing docker is the most reliable way to build from source.\n\n```shell\ndocker build .\n```\n\nIf you're using Debian 12, run the following command to download the dependencies and build the tool:\n\n```shell\nsudo ./cloud_build/debianBuild.sh\n```\n\nOtherwise, follow these steps:\n\n1. Download the source from the Releases tab or check out the repo.\n2. Make sure that you have the following dependencies installed:\n\n  - g++ \u003e=8\n  - cmake \u003e=3\n  - boost \u003e=1.69: https://www.boost.org/users/history/version_1_69_0.html\n  - dcmtk source ==3.6.6: https://github.com/DCMTK/dcmtk/archive/refs/tags/DCMTK-3.6.6.zip\n  - openslide \u003e=3.4.1\n  - libjpeg_turbo \u003e= 2.1.2 https://github.com/libjpeg-turbo/libjpeg-turbo/archive/refs/tags/2.1.2.zip\n  - openjpeg \u003e= 2.3.0\n  - jsoncpp \u003e= 1.8.0\n  - OpenCV \u003e= 4.5.4.     https://github.com/opencv/opencv/archive/refs/tags/4.5.4.zip\n  - abseil \u003e= 20211102.0 https://github.com/abseil/abseil-cpp/archive/refs/tags/20211102.0.zip\n\n3. Run the following commands:\n\n```shell\nmkdir build\ncd build\ncp -R %dcmtkDir% ./dcmtk-3.6.6\ncmake ..\nmake -j%threads%\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgooglecloudplatform%2Fwsi-to-dicom-converter","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgooglecloudplatform%2Fwsi-to-dicom-converter","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgooglecloudplatform%2Fwsi-to-dicom-converter/lists"}