Update documentation

Author: hackermd

README.md

@@ -1,46 +1,34 @@
 [![Build Status](https://travis-ci.com/mghcomputationalpathology/dicom-microscopy-viewer.svg?branch=master)](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/).
+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.
 
-## Installation
+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.
 
-Install the [dicom-microscopy-viewer](https://www.npmjs.com/package/dicom-microscopy-viewer) package using the `npm` package manager:
+## Features
 
-```None
-npm install dicom-microscopy-viewer
-```
+* 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
 
-## Building and testing
+## Live demo
 
-Build and test code locally:
+Check out the online examples at [microscopy.dcmjs.org](https://microscopy.dcmjs.org/).
 
-```None
-git clone https://github.com/mghcomputationalpathology/dicom-microscopy-viewer ~/dicom-microscopy-viewer
-cd ~/dicom-microscopy-viewer
-npm install
-npm run build
-npm test
-```
+## Documentation
 
-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/)).
+The online Application Programming Interface (API) documentation is available at [mghcomputationalpathology.github.io/dicom-microscopy-viewer](https://mghcomputationalpathology.github.io/dicom-microscopy-viewer/).
 
-Build the documentation:
+## Getting started
 
-```None
-npm run generateDocs
-```
+Take a look at the examples in the `/examples` directory.
+They are also available online at [microscopy.dcmjs.org](https://microscopy.dcmjs.org/).
 
-## Usage
+### Basic usage
 
 ```html
 <script type="text/javascript" src="https://unpkg.com/dicom-microscopy-viewer"></script>
@@ -53,7 +41,6 @@ DICOM JSON Model](http://dicom.nema.org/medical/dicom/current/output/chtml/part1
 
 * 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});
@@ -73,15 +60,16 @@ client.searchForInstances(searchInstanceOptions).then((instances) => {
       sopInstanceUID,
     };
     const promise = client.retrieveInstanceMetadata(retrieveInstanceOptions).then(metadata => {
-      const image = DICOMMicroscopyViewer.metadata.formatMetadata(metadata[0]);
-      if (image.ImageType[2] === "VOLUME") {
+      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
@@ -90,27 +78,6 @@ client.searchForInstances(searchInstanceOptions).then((instances) => {
 });
 ```
 
-## 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):
@@ -134,27 +101,41 @@ Please cite the following article when using the viewer for scientific studies:
 
 ```
 
-## Documentation
+## Installation
 
-The online Application Programming Interface (API) documentation is available at [mghcomputationalpathology.github.io/dicom-microscopy-viewer](https://mghcomputationalpathology.github.io/dicom-microscopy-viewer/).
+Install the [dicom-microscopy-viewer](https://www.npmjs.com/package/dicom-microscopy-viewer) package using the `npm` package manager:
 
-## Getting started
+```None
+npm install dicom-microscopy-viewer
+```
 
-Take a look at the examples in the `/examples` directory.
-They are also available online at [microscopy.dcmjs.org](https://microscopy.dcmjs.org/).
+## 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
+```
 
 ## 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))
+* [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/)
-
-## Troubleshooting
-### Overview map not responsive: 
-Some interactions could cause side effects on the viewer's instance of OverviewMap since it also uses the same interactions in the map.
-If you enable the 'draw' interaction, the overview map will lost its ability to instantly update
-the map when changed.
+* [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/)