README.md

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Content

1. Hello AMI
2. Features
3. Usage
4. Developer corner
5. Change log
6. Credits
7. Citations

Hello AMI

	Lesson 00: Load Load DICOM Data and get a nice Series/Stack/Frame structure.		Lesson 01: Visualize 3D Look at the data we loaded in 3D.
	Lesson 02: Mesh Add a mesh to the scene.		Lesson 03: Visualize 2D Look at the data in 2D.
	Lesson 04: Labelmap Overlays on top of you data.		Lesson 05: TRK TRK - coming soon.
	Lesson 06: Volume Rendering Volume Rendering.		Lesson 07: Lookup tables Lookup Tables - coming soon.
	Lesson 08: Custom progress bar Custom progress bars.

(more) Advanced demos

Volume rendering, 2D viewer, arbitrary reslicing and more examples and advanced demos there!

Features

✅ READY 🔶 IN PROGRESS OR LIMITED SUPPORT ❌ ON ROADMAP

Capabilities	Volumes	Meshes	Widgets
✅ 2D Visulization	✅ Dicom	✅ VTK (THREEJS)	🔶 Handle (2D/3D)
✅ 3D Visualization	✅ NRRD	✅ STL (THREEJS)	🔶 Probe (2D/3D)
✅ Volume Rendering	✅ Nifti	✅ TRK	🔶 Ruler (2D/3D)
✅ Lookup Tables	✅ MHD/(Z)RAW	✅ FSM	🔶 Orientation (2D/3D)
✅ Label Maps	✅ MGH/MGZ	❌ CURV	🔶 Angle (2D/3D)
	❌ JPEG

Usage

Pre-requisites

• ES2015 promises support. (consider using polyfills if needed)
• Load THREEJS your index.html BEFORE AMI.

<script src="https://cdnjs.cloudflare.com/ajax/libs/three.js/r81/three.js"></script>

Yarn

$> yarn add ami.js

Note: you might need to include babel transforms in you build process.

// app.js
import * as AMI form 'ami.js';
window.console.log('Ready to rock!!');

ami.js

Check-out the lessons to get started quickly.

New: Use the new factory not to have to include three in index.html.

import * as THREE from 'three';
import {stackHelperFactory} from 'ami.js';

const StackHelper = stackHelperFactory(THREE);
const stackHelper = new StackHelper();

Add AMI in your index.html after THREEJS.

<!-- index.html -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/three.js/r81/three.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/ami.js/0.0.12/ami.min.js"></script>
<script src="app.js"></script>

#app.js
const AMI = AMI;
window.console.log('Ready to rock!!');

Developer corner

Get the source code and related packages.

$> git clone https://github.com/FNNDSC/ami.git
$> cd ami
$> yarn install

To run examples (browserify/babelify/serve the example)

$> yarn example <examples name>

#run the geometries_slice example
$> yarn example geometries_slice

Build standalone library to lib/

$> yarn build:ami

Build minified standalone version run

$> yarn build:ami:prod

Tests

$> yarn test

Documentation

$> yarn doc

Build and deploy dist/ to gh-pages

$> yarn deploy

Find out more about the API.

Change log

Credits

AMI would not exist without them:

THREEJS

• Base components such as Vectors, Matrices and Objects3D.
• HTML template for example page.
• Author(s): mrdoob

DicomParser

• DICOM parsing relies on it.
• Author(s): chafey

CornerstoneWADOImageLoader

• Was used to figure out how to use the dicom parser properly.
• Author(s): chafey

NIFTI-Reader-JS

• Nifti parsing relies on it.
• Author(s): rii-mango

NRRD-JS

• NRRD parsing relies on it.
• Author(s): jaspervdg

JPEGLosslessDecoderJS

• JPEG Lossless Decoder for DICOM images
• Author(s): rii-mango

Image-JPEG2000

• JPEG 2000 Decoder for DICOM images
• Author(s): jpambrun, mozilla

Pako

• GZ file decompression
• Author(s): nodeca

Citations

2017

• From brain imaging to weather imaging - McCaie - informaticslab, Met Office (blog post)
• Medical imaging in the browser with the A* Medical Imaging (AMI) toolkit. - Rannou et al. - ESMRMB 2017 (poster)
• Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization - Bernal-Rusiel et al. - Frontiers in Neuroinformatics 2017 (article)

2016

• Volume Visualization Tools for Medical Applications in Ubiquitous Platforms - Arbelaiz et al. - LNICST 2016 (article)
• Interoperable communication of quantitative image analysis results using DICOM standard (DICOM4QI) - Fedorov et al. - RSNA 2016 (poster)