dicom-microscopy-viewer：基于Web的DICOM可见光整个幻灯片显微镜图像查看器

[](https://travis-ci.com/mghcomputationalpathology/dicom-microscopy-viewer) # DICOM Microscopy Viewer Vanilla JS library for web-based visualization of [DICOM VL Whole Slide Microscopy Image](http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.32.8.html) datasets. ## Motivation and implementation The library is intended to provide a lightweight and standard-compliant viewer for microscopy images in DICOM format. The viewer relies on [Openlayers](http://openlayers.org/) for rendering pyramid images and dynamically retrieves pyramid tiles (image frames) via [DICOMweb WADO-RS](https://www.dicomstandard.org/dicomweb/retrieve-wado-rs-and-wado-uri/) using [dicomweb-client](https://github.com/mghcomputationalpathology/dicomweb-client). However, the viewer API fully abstracts the underlying rendering library and doesn't expose the lower level Openlayers API directly, such that another rendering library could in principle be used in the future if this would be of advantage. ## Live demo Check out the online examples at [microscopy.dcmjs.org](https://microscopy.dcmjs.org/). ## Installation Install the [dicom-microscopy-viewer](https://www.npmjs.com/package/dicom-microscopy-viewer) package using the `npm` package manager: ```None npm install dicom-microscopy-viewer ``` ## Building and testing Build and test code locally: ```None git clone https://github.com/mghcomputationalpathology/dicom-microscopy-viewer ~/dicom-microscopy-viewer cd ~/dicom-microscopy-viewer npm install npm run build npm test ``` We use [rollup](https://rollupjs.org/guide/en) for bundling and [mochify](https://github.com/mantoni/mochify.js) for testing (based on [mocha](https://mochajs.org/) and [chai](http://www.chaijs.com/)). Build the documentation: ```None npm run generateDocs ``` ## Usage ```html <script type="text/javascript" src="https://unpkg.com/dicom-microscopy-viewer"></script> ``` The viewer can be embedded in any website, one only needs to * Create an instance of the `viewer.VolumeViewer`. The constructor requires an instance of `DICOMwebClient` for retrieving frames from the archive as well as the metadata for each DICOM image instance formatted according to the [ DICOM JSON Model](http://dicom.nema.org/medical/dicom/current/output/chtml/part18/sect_F.2.html). * Call the `render()` method, passing it the HTML element (or the name of the element), which shall contain the viewport. ```js const url = 'http://localhost:8080/dicomweb'; const client = new DICOMwebClient.api.DICOMwebClient({url}); const studyInstanceUID = '1.2.3.4'; const seriesInstanceUID = '1.2.3.5'; const searchInstanceOptions = { studyInstanceUID, seriesInstanceUID }; client.searchForInstances(searchInstanceOptions).then((instances) => { const promises = [] for (let i = 0; i < instances.length; i++) { const sopInstanceUID = instances[i]["00080018"]["Value"][0]; const retrieveInstanceOptions = { studyInstanceUID, seriesInstanceUID, sopInstanceUID, }; const promise = client.retrieveInstanceMetadata(retrieveInstanceOptions).then(metadata => { const imageType = metadata[0]["00080008"]["Value"]; if (imageType[2] === "VOLUME") { return(metadata[0]); } }); promises.push(promise); } return(Promise.all(promises)); }).then(metadata => { metadata = metadata.filter(m => m); const viewer = new DICOMMicroscopyViewer.viewer.VolumeViewer({ client, metadata }); viewer.render({container: 'viewport'}); }); ``` ## Status **Investigational use only!** The viewer allows visualization of *VL Whole Slide Microscopy Image* datasets stored in a [DICOMweb](https://www.dicomstandard.org/dicomweb/) compatible archive. It leverages the [dicomweb-client](https://github.com/dcmjs-org/dicomweb-client) JavaScript library to retrieve data from the archive. ### Features * Display of different image types: `VOLUME`, `OVERVIEW`, `LABEL` * Server-side rendering of images with inclusion of ICC profiles for color reproducibility * Client-side assembly of concatenations * Vector graphic annotation of regions of interest (ROI) based on 3-dimensional spatial coordinates (SCOORD3D): `POINT`, `MULTIPOINT`, `POLYLINE`, `POLYGON`, `ELLIPSE`, `ELLIPSOID` ### Limitations Currently, the viewer only supports * Brightfield illumination (no fluorescence) * 2D images (no z-stacks) ## Citation Please cite the following article when using the viewer for scientific studies: [Herrmann et al. J Path Inform. 2018](http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2018;volume=9;issue=1;spage=37;epage=37;aulast=Herrmann): ```None @article{jpathinform-2018-9-37, Author={ Herrmann, M. D. and Clunie, D. A. and Fedorov A. and Doyle, S. W. and Pieper, S. and Klepeis, V. and Le, L. P. and Mutter, G. L. and Milstone, D. S. and Schultz, T. J. and Kikinis, R. and Kotecha, G. K. and Hwang, D. H. and Andriole, K, P. and Iafrate, A. J. and Brink, J. A. and Boland, G. W. and Dreyer, K. J. and Michalski, M. and Golden, J. A. and Louis, D. N. and Lennerz, J. K. }, Title={Implementing the {DICOM} standard for digital pathology}, Journal={Journal of Pathology Informatics}, Year={2018}, Number={1}, Volume={9}, Number={37} } ``` ## Documentation The online Application Programming Interface (API) documentation is available at [mghcomputationalpathology.github.io/dicom-microscopy-viewer](https://mghcomputationalpathology.github.io/dicom-microscopy-viewer/). ## Getting started Take a look at the examples in the `/examples` directory. They are also available online at [microscopy.dcmjs.org](https://microscopy.dcmjs.org/). ## Support The developers gratefully acknowledge their reseach support: * Open Health Imaging Foundation ([OHIF](http://ohif.org)) * Quantitative Image Informatics for Cancer Research ([QIICR](http://qiicr.org)) * [Radiomics](http://radiomics.io) * The [Neuroimage Analysis Center](http://nac.spl.harvard.edu) * The [National Center for Image Guided Therapy](http://ncigt.org) * The [MGH & BWH Center for Clinical Data Science](https://www.ccds.io/)