<p align="center"> <img src="https://user-images.githubusercontent.com/214063/46479857-4cd66e80-c7f0-11e8-9585-5748409c9490.png" width="60%"> </p> <p align="center"> <a href="https://travis-ci.org/FNNDSC/ami"> <img src="https://travis-ci.org/FNNDSC/ami.svg?branch=master" alt="Build Status"> </a> <a href="https://cdnjs.com/libraries/ami.js"> <img src="https://img.shields.io/cdnjs/v/ami.js.svg" alt="CDNJS Version"> </a> <a href="https://www.npmjs.com/package/ami.js"> <img src="https://img.shields.io/npm/v/ami.js/next.svg" alt="NPM Version"> </a> <a href="https://join.slack.com/t/amijs/shared_invite/enQtNDU5MTQ1OTMzMDYxLWE5NTBlMWM2ZjhlYjVkNzZmZDg3YTdjYzQxYWI3NTY4NmIyZGY5MmQyYjE4NmQyOGZkY2NlYzY1MTk5ZDFmNWY"> <img src="https://img.shields.io/badge/slack-join-blue.svg" alt="Slack"> </a> </p>

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Content

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

Hello AMI

<table> <tr> <!-- Lesson 00 --> <td valign="middle" width="100"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/00' target=_blank> <img src="https://unpkg.com/ami.js@next/lessons/00/assets/thumbnail-128x128.jpg" alt="lesson00" title="Click me!"> </a> </td> <td valign="top" width="326"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/00'> <b>Lesson 00: Load</b> </a> <div> Load DICOM Data and get a nice Series/Stack/Frame structure. </div> </td> <!-- Lesson 01 --> <td valign="middle" width="100"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/01' target=_blank> <img src="https://cloud.githubusercontent.com/assets/214063/14734707/8963a142-086c-11e6-99e2-35125f5ebb83.gif" style="width:128x, height:128px" alt="lesson01" title="Click me!"> </a> </td> <td valign="top" width="326"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/01'> <b>Lesson 01: Visualize 3D</b> </a> <div> Look at the data we loaded in 3D. </div> </td> </tr> <tr> <!-- Lesson 02 --> <td valign="middle" width="100"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/02' target=_blank> <img src="https://cloud.githubusercontent.com/assets/214063/14734782/1aa3006c-086d-11e6-9f56-6476e5ac6188.gif" style="width:128x, height:128px" alt="lesson00" title="Click me!"> </a> </td> <td valign="top" width="326"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/02'> <b>Lesson 02: Mesh</b> </a> <div> Add a mesh to the scene. </div> </td> <!-- Lesson 03 --> <td valign="middle" width="100"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/03' target=_blank> <img src="https://cloud.githubusercontent.com/assets/214063/14734860/99882c22-086d-11e6-99ae-16b7e5371f40.gif" style="width:128x, height:128px" alt="lesson00" title="Click me!"> </a> </td> <td valign="top" width="326"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/03'> <b>Lesson 03: Visualize 2D</b> </a> <div> Look at the data in 2D. </div> </td> </tr> <tr> <!-- Lesson 04 --> <td valign="middle" width="100"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/04' target=_blank> <img src="https://cloud.githubusercontent.com/assets/214063/16259390/b04a7d96-3862-11e6-8937-3019b913a21f.gif" style="width:128x, height:128px" alt="lesson00" title="Click me!"> </a> </td> <td valign="top" width="326"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/04' target=_blank> <b>Lesson 04: Labelmap</b> </a> <div> Overlays on top of you data. </div> </td> <!-- Lesson 05 --> <td valign="middle" width="100"> <!--<a href='http://jsfiddle.net/gh/get/library/pure/fnndsc/ami/tree/master/lessons/02#run' target=_blank>--> <!-- <img src="https://cdn.rawgit.com/fnndsc/ami/master/lessons/02/thumbnail-128x128.jpg" alt="lesson00" title="Click me!">--> <!-- <img src="http://xtk.github.com/fiddlelogo_small2.png">--> <!--</a>--> </td> <td valign="top" width="326"> <!--<a href='http://jsfiddle.net/gh/get/library/pure/fnndsc/ami/tree/master/lessons/02#run'>--> <b>Lesson 05: TRK</b> <!--</a>--> <div> TRK - coming soon. </div> </td> </tr> <tr> <!-- Lesson 06 --> <td valign="middle" width="100"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/06' target=_blank> <img src="https://cloud.githubusercontent.com/assets/214063/20212355/fdf512b2-a802-11e6-884d-bfafd0a1ec7d.gif" style="width:128x, height:128px" alt="lesson00" title="Click me!"> </a> </td> <td valign="top" width="326"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/06'> <b>Lesson 06: Volume Rendering</b> </a> <div> Volume Rendering. </div> </td> <!-- Lesson 07 --> <td valign="middle" width="100"> <!--<a href='http://jsfiddle.net/gh/get/library/pure/fnndsc/ami/tree/master/lessons/02#run' target=_blank>--> <!-- <img src="https://cdn.rawgit.com/fnndsc/ami/master/lessons/02/thumbnail-128x128.jpg" alt="lesson00" title="Click me!">--> <!-- <img src="http://xtk.github.com/fiddlelogo_small2.png">--> <!--</a>--> </td> <td valign="top" width="326"> <!--<a href='http://jsfiddle.net/gh/get/library/pure/fnndsc/ami/tree/master/lessons/02#run'>--> <b>Lesson 07: Lookup tables</b> <!--</a>--> <div> Lookup Tables - coming soon. </div> </td> </tr> <tr> <!-- Lesson 08 --> <td valign="middle" width="100"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/08' target=_blank> <img src="https://cloud.githubusercontent.com/assets/214063/20597899/9b7ec102-b246-11e6-804b-be8ac6dc9a68.gif" style="width:128x, height:128px" alt="lesson00" title="Click me!"> </a> </td> <td valign="top" width="326"> <a href='https://codesandbox.io/s/github/FNNDSC/ami/tree/master/lessons/08'> <b>Lesson 08: Custom progress bar</b> </a> <div> Custom progress bars. </div> </td> </tr> </table>

(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.

hmtlCopy

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

Yarn

bashCopy

$> yarn add ami.js

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

javascriptCopy

// 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.

javascriptCopy
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.

htmlCopy

<!-- 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.

bashCopy

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

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

bashCopy

$> yarn example <examples name>

#run the geometries_slice example
$> yarn example geometries_slice

Build standalone library to lib/

bashCopy

$> yarn build:ami

Build minified standalone version run

bashCopy

$> yarn build:ami:prod

Tests

bashCopy

$> yarn test

Documentation

bashCopy

$> yarn doc

Build and deploy dist/ to gh-pages

bashCopy

$> 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)