DICOM Microscopy Viewer
Vanilla JS library for web-based visualization of DICOM VL Whole Slide Microscopy Image datasets.
The viewer allows visualization of slide microscopy images stored in a DICOMweb compatible archive. It leverages the dicomweb-client JavaScript library to retrieve data from the archive.
Features
- Display of different image types:
VOLUME,OVERVIEW,LABEL - Annotation of regions of interest (ROI) as vector graphics based on 3-dimensional spatial coordinates (SCOORD3D):
POINT,MULTIPOINT,POLYLINE,POLYGON,ELLIPSE,ELLIPSOID - Assembly of concatenations
- Decoding of compressed pixel data, supporting baseline JPEG, JPEG 2000 and JPEG-LS codecs
- Additive blending and coloring of monochromatic images of multiple optical paths (channels), supporting highly-multiplexed immunofluorescence imaging
Live demo
Check out the online examples at microscopy.dcmjs.org.
Documentation
The online Application Programming Interface (API) documentation is available at 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.
Basic usage
<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 ofDICOMwebClientfor retrieving frames from the archive as well as the metadata for each DICOM image instance formatted according to the DICOM JSON Model. -
Call the
render()method, passing it the HTML element (or the name of the element), which shall contain the viewport.
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'});
});Citation
Please cite the following article when using the viewer for scientific studies: Herrmann et al. J Path Inform. 2018:
@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}
}
Installation
Install the dicom-microscopy-viewer package using the npm package manager:
npm install dicom-microscopy-viewer
Building & Testing
Build code locally:
git clone https://github.com/mghcomputationalpathology/dicom-microscopy-viewer ~/dicom-microscopy-viewer
cd ~/dicom-microscopy-viewer
npm install
npm run build
test code locally:
git clone https://github.com/mghcomputationalpathology/dicom-microscopy-viewer ~/dicom-microscopy-viewer
cd ~/dicom-microscopy-viewer
npm install
npm test
We use rollup for bundling and Jest for testing.
Build the documentation:
npm run generateDocs
Support
The developers gratefully acknowledge their reseach support: