feat: cornerstone3D stack and volume viewports (#2787)
* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <erik.sweed@gmail.com> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <erik.sweed@gmail.com> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <ar.sedghi@gmail.com> Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
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---
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sidebar_position: 1
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sidebar_label: DICOMweb
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---
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# DICOMweb
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## Set up a local DICOM server
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ATTENTION! Already have a remote or local server? Skip to the
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[configuration section](#configuration-learn-more) below.
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While the OHIF Viewer can work with any data source, the easiest to configure
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are the ones that follow the [DICOMWeb][dicom-web] spec.
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1. Choose and install an Image Archive
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2. Upload data to your archive (e.g. with DCMTK's [storescu][storescu] or your
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archive's web interface)
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3. Keep the server running
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For our purposes, we will be using `Orthanc`, but you can see a list of
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[other Open Source options](#open-source-dicom-image-archives) below.
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### Requirements
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- Docker
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- [Docker for Mac](https://docs.docker.com/docker-for-mac/)
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- [Docker for Windows (recommended)](https://docs.docker.com/docker-for-windows/)
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- [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/)
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_Not sure if you have `docker` installed already? Try running `docker --version`
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in command prompt or terminal_
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> If you are using `Docker Toolbox` you need to change the _PROXY_DOMAIN_
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> parameter in _platform/viewer/package.json_ to http://192.168.99.100:8042 or
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> the ip docker-machine ip throws. This is the value [`WebPack`][webpack-proxy]
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> uses to proxy requests
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## Open Source DICOM Image Archives
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There are a lot of options available to you to use as a local DICOM server. Here
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are some of the more popular ones:
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| Archive | Installation |
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| --------------------------------------------- | ---------------------------------- |
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| [DCM4CHEE Archive 5.x][dcm4chee] | [W/ Docker][dcm4chee-docker] |
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| [Orthanc][orthanc] | [W/ Docker][orthanc-docker] |
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| [DICOMcloud][dicomcloud] (**DICOM Web only**) | [Installation][dicomcloud-install] |
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| [OsiriX][osirix] (**Mac OSX only**) | Desktop Client |
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| [Horos][horos] (**Mac OSX only**) | Desktop Client |
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_Feel free to make a Pull Request if you want to add to this list._
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Below, we will focus on `DCM4CHEE` and `Orthanc` usage:
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### Running Orthanc
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_Start Orthanc:_
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```bash
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# Runs orthanc so long as window remains open
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yarn run orthanc:up
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```
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_Upload your first Study:_
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1. Navigate to
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[Orthanc's web interface](http://localhost:8042/app/explorer.html) at
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`http://localhost:8042/app/explorer.html` in a web browser.
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2. In the top right corner, click "Upload"
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3. Click "Select files to upload..." and select one or more DICOM files
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4. Click "Start the upload"
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#### Orthanc: Learn More
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You can see the `docker-compose.yml` file this command runs at
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[`<project-root>/.docker/Nginx-Orthanc/`][orthanc-docker-compose], and more on
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Orthanc for Docker in [Orthanc's documentation][orthanc-docker].
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#### Connecting to Orthanc
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Now that we have a local Orthanc instance up and running, we need to configure
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our web application to connect to it. Open a new terminal window, navigate to
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this repository's root directory, and run:
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```bash
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# If you haven't already, enable yarn workspaces
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yarn config set workspaces-experimental true
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# Restore dependencies
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yarn install
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# Run our dev command, but with the local orthanc config
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yarn run dev:orthanc
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```
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#### Configuration: Learn More
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> For more configuration fun, check out the
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> [Essentials Configuration](../index.md) guide.
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Let's take a look at what's going on under the hood here. `yarn run dev:orthanc`
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is running the `dev:orthanc` script in our project's `package.json` (inside
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`platform/viewer`). That script is:
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```js
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cross-env NODE_ENV=development PROXY_TARGET=/dicom-web PROXY_DOMAIN=http://localhost:8042 APP_CONFIG=config/docker_nginx-orthanc.js webpack-dev-server --config .webpack/webpack.pwa.js -w
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```
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- `cross-env` sets three environment variables
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- PROXY_TARGET: `/dicom-web`
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- PROXY_DOMAIN: `http://localhost:8042`
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- APP_CONFIG: `config/docker_nginx-orthanc.js`
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- `webpack-dev-server` runs using the `.webpack/webpack.pwa.js` configuration
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file. It will watch for changes and update as we develop.
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`PROXY_TARGET` and `PROXY_DOMAIN` tell our development server to proxy requests
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to `Orthanc`. This allows us to bypass CORS issues that normally occur when
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requesting resources that live at a different domain.
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The `APP_CONFIG` value tells our app which file to load on to `window.config`.
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By default, our app uses the file at
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`<project-root>/platform/viewer/public/config/default.js`. Here is what that
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configuration looks like:
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```js
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window.config = {
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routerBasename: '/',
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extensions: [],
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modes: [],
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showStudyList: true,
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dataSources: [
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{
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friendlyName: 'dcmjs DICOMWeb Server',
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namespace: '@ohif/extension-default.dataSourcesModule.dicomweb',
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sourceName: 'dicomweb',
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configuration: {
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name: 'DCM4CHEE',
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wadoUriRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/wado',
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qidoRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs',
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wadoRoot: 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs',
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qidoSupportsIncludeField: true,
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supportsReject: true,
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imageRendering: 'wadors',
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thumbnailRendering: 'wadors',
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enableStudyLazyLoad: true,
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supportsFuzzyMatching: true,
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supportsWildcard: true,
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},
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},
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],
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defaultDataSourceName: 'dicomweb',
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};
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```
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To learn more about how you can configure the OHIF Viewer, check out our
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[Configuration Guide](../index.md).
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### Running DCM4CHEE
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dcm4che is a collection of open source applications for healthcare enterprise
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written in Java programming language which implements DICOM standard. dcm4chee
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(extra 'e' at the end) is dcm4che project for an Image Manager/Image Archive
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which provides storage, retrieval and other functionalities. You can read more
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about dcm4chee in their website [here](https://www.dcm4che.org/)
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DCM4chee installation is out of scope for these tutorials and can be found
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[here](https://github.com/dcm4che/dcm4chee-arc-light/wiki/Run-minimum-set-of-archive-services-on-a-single-host)
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An overview of steps for running OHIF Viewer using a local DCM4CHEE is shown
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below:
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<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
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<iframe src="https://player.vimeo.com/video/557570043?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
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</div>
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[dcm4chee]: https://github.com/dcm4che/dcm4chee-arc-light
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[dcm4chee-docker]:
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https://github.com/dcm4che/dcm4chee-arc-light/wiki/Running-on-Docker
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[orthanc]: https://www.orthanc-server.com/
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[orthanc-docker]: http://book.orthanc-server.com/users/docker.html
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[dicomcloud]: https://github.com/DICOMcloud/DICOMcloud
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[dicomcloud-install]: https://github.com/DICOMcloud/DICOMcloud#running-the-code
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[osirix]: http://www.osirix-viewer.com/
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[horos]: https://www.horosproject.org/
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[default-config]:
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https://github.com/OHIF/Viewers/blob/master/platform/viewer/public/config/default.js
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[html-templates]:
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https://github.com/OHIF/Viewers/tree/master/platform/viewer/public/html-templates
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[config-files]:
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https://github.com/OHIF/Viewers/tree/master/platform/viewer/public/config
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