Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

https://github.com/ImagingDataCommons/dicom-microscopy-viewer

Web-based DICOM slide microscopy viewer library
https://github.com/ImagingDataCommons/dicom-microscopy-viewer

dicom dicom-json dicomweb idc-viewers javascript npm openlayers

Last synced: 9 days ago
JSON representation

Web-based DICOM slide microscopy viewer library

Lists

README 

        
[![Build Status](https://github.com/imagingdatacommons/dicom-microscopy-viewer/actions/workflows/run_unit_tests.yml/badge.svg)](https://github.com/imagingdatacommons/dicom-microscopy-viewer/actions)

[![NPM version](https://badge.fury.io/js/dicom-microscopy-viewer.svg)](http://badge.fury.io/js/dicom-microscopy-viewer)

![NPM downloads per month](https://img.shields.io/npm/dm/dicom-microscopy-viewer?color=blue)



# 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 and derived information.



The viewer allows visualization of slide microscopy images 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`/`THUMBNAIL`, `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

* Correction of color images using ICC profiles

* Additive blending and coloring of monochromatic images of multiple optical paths (channels), supporting highly-multiplexed immunofluorescence imaging

* Overlay of image analysis results in the form of [DICOM Segmentation](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.51.html), [Parametric Map](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.75.html), [Comprehensive 3D SR](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.35.13.html), or [Microscopy Bulk Simple Annotations](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.87.html)



## Documentation



Documentation of the JavaScript Application Programming Interface (API) is available online at [imagingdatacommons.github.io/dicom-microscopy-viewer](https://imagingdatacommons.github.io/dicom-microscopy-viewer/).



## Getting started



Note that the *dicom-microscopy-viewer* package is **not** a viewer application, it is a library to build viewer applications.



Below is an example for the most basic usage: a web page that displays a collection of DICOM VL Whole Slide Microscopy Image instances of a digital slide.

For more advanced usage, take a look at the [Slim](https://github.com/imagingdatacommons/slim) viewer.



## Packaging



The library is packaged as two different builds, one using dynamic import, and the other bundling into one 

larger library.  The dynamic import version uses a public path of `/dicom-microscopy-viewer/` so that they can be used by simply adding an alias to the appropriate version, and then deploying that version.  In a straight web application, this can be loaded as:



```javascript

   const DICOMMicroscopyViewer = (await('/dicom-microscopy-viewer/dicomMicroscopyViewer.min.js')).default

```



The point of using the sub-directory here is to isolate the dependencies that unique to `dicom-microscopy-viewer`.



### Basic usage



The viewer can be embedded in any website, one only needs to



* Create an instance of [VolumeImageViewer](https://imagingdatacommons.github.io/dicom-microscopy-viewer/viewer.VolumeImageViewer.html). The constructor requires an instance of `DICOMwebClient` for retrieving frames from the archive as well as the metadata for each DICOM image as an instance of [VLWholeSlideMicroscopyImage](https://imagingdatacommons.github.io/dicom-microscopy-viewer/metadata.VLWholeSlideMicroscopyImage.html).



* Call the `render()` method, passing it the HTML element (or the name of the element), which shall contain the viewport.



```js

import * as DICOMMicroscopyViewer from 'dicom-microscopy-viewer';

import * as DICOMwebClient from 'dicomweb-client';



// Construct client instance

const client = new DICOMwebClient.api.DICOMwebClient({

  url: 'http://localhost:8080/dicomweb'

});



// Retrieve metadata of a series of DICOM VL Whole Slide Microscopy Image instances

const retrieveOptions = {

  studyInstanceUID: '1.2.3.4',

  seriesInstanceUID: '1.2.3.5'

};

client.retrieveSeriesMetadata(retrieveOptions).then((metadata) => {

  // Parse, format, and filter metadata

  const volumeImages = []

  metadata.forEach(m => {

    const image = new DICOMMicroscopyViewer.metadata.VLWholeSlideMicroscopyImage({

      metadata: m

    })

    const imageFlavor = image.ImageType[2]

    if (imageFlavor === 'VOLUME' || imageFlavor === 'THUMBNAIL') {

      volumeImages.push(image)

    }

  })



  // Construct viewer instance

  const viewer = new DICOMMicroscopyViewer.viewer.VolumeViewer({

    client,

    metadata: volumeImages

  });



  // Render viewer instance in the "viewport" HTML element

  viewer.render({ container: 'viewport' });

});

```



## 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}

}

```



## 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

```



## Development & Testing



We use [Babel](https://babeljs.io/) to compile (transpile), [webpack](https://webpack.js.org/) to bundle, and [Jest](https://github.com/facebook/jest) to test JavaScript code.



Get the source code by cloning the git repository:



```None

git clone https://github.com/imagingdatacommons/dicom-microscopy-viewer

cd dicom-microscopy-viewer

```



Install dependencies and build the package:



```None

npm install

npm run build

```



Run tests:



```None

npm run test

```



Build the API documentation:



```None

npm run generateDocs

```



## 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)

* [Imaging Data Commons (IDC)](https://datacommons.cancer.gov/repository/imaging-data-commons)

* [Neuroimage Analysis Center](http://nac.spl.harvard.edu)

* [National Center for Image Guided Therapy](http://ncigt.org)

* [MGH & BWH Center for Clinical Data Science (CCDS)](https://www.ccds.io/)