@edsilv/ami.js

<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> ---------- ### Content 1. [Hello AMI](#hello-ami) 2. [Features](#features) 3. [Usage](#yarn) 4. [Developer corner](#developer-corner) 5. [Change log](#change-log) 6. [Credits](#credits) 7. [Citations](#citations) ## Hello AMI <table> <tr>  <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>  <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>  <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>  <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>  <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>  <td valign="middle" width="100">     </td> <td valign="top" width="326">  <b>Lesson 05: TRK</b>  <div> TRK - coming soon. </div> </td> </tr> <tr>  <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>  <td valign="middle" width="100">     </td> <td valign="top" width="326">  <b>Lesson 07: Lookup tables</b>  <div> Lookup Tables - coming soon. </div> </td> </tr> <tr>  <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](https://fnndsc.github.io/ami)! ## 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. ```hmtl <script src="https://cdnjs.cloudflare.com/ajax/libs/three.js/r81/three.js"></script> ``` ### Yarn ```bash $> yarn add ami.js ``` *Note*: you might need to include [babel](https://github.com/babel/babel) transforms in you build process. ```javascript // app.js import * as AMI form 'ami.js'; window.console.log('Ready to rock!!'); ``` ### ami.js Check-out the [lessons](#lessons) to get started quickly. **New:** Use the new factory not to have to include `three` in index.html. ```javascript 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. ```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. ```bash $> git clone https://github.com/FNNDSC/ami.git $> cd ami $> yarn install ``` To run examples (browserify/babelify/serve the example) ```bash $> yarn example <examples name> #run the geometries_slice example $> yarn example geometries_slice ``` Build standalone library to `lib/` ```bash $> yarn build:ami ``` Build minified standalone version run ```bash $> yarn build:ami:prod ``` Tests ```bash $> yarn test ``` Documentation ```bash $> yarn doc ``` Build and deploy dist/ to gh-pages ```bash $> yarn deploy ``` Find out more about the [API](https://fnndsc.github.io/ami/doc). # [Change log](https://github.com/FNNDSC/ami/releases) # Credits AMI would not exist without them: ##### [THREEJS](https://github.com/mrdoob/three.js/) - Base components such as Vectors, Matrices and Objects3D. - HTML template for example page. - Author(s): [mrdoob](https://github.com/mrdoob) ##### [DicomParser](https://github.com/chafey/dicomParser) - DICOM parsing relies on it. - Author(s): [chafey](https://github.com/chafey) ##### [CornerstoneWADOImageLoader](https://github.com/chafey/cornerstoneWADOImageLoader) - Was used to figure out how to use the dicom parser properly. - Author(s): [chafey](https://github.com/chafey) ##### [NIFTI-Reader-JS](https://github.com/rii-mango/NIFTI-Reader-JS) - Nifti parsing relies on it. - Author(s): [rii-mango](https://github.com/rii-mango) ##### [NRRD-JS](https://github.com/scijs/nrrd-js) - NRRD parsing relies on it. - Author(s): [jaspervdg](https://github.com/jaspervdg) ##### [JPEGLosslessDecoderJS](https://github.com/rii-mango/JPEGLosslessDecoderJS) - JPEG Lossless Decoder for DICOM images - Author(s): [rii-mango](https://github.com/rii-mango) ##### [Image-JPEG2000](https://github.com/OHIF/image-JPEG2000) - JPEG 2000 Decoder for DICOM images - Author(s): [jpambrun](https://github.com/jpambrun), [mozilla](https://github.com/mozilla/pdf.js/) ##### [Pako](https://github.com/nodeca/pako) - GZ file decompression - Author(s): [nodeca](https://github.com/nodeca) # Citations ### 2017 - [From brain imaging to weather imaging - McCaie - informaticslab, Met Office (blog post)](http://www.informaticslab.co.uk/side-projects/weather/3d/visualisations/2017/04/04/from-brain-imaging-to-weather-imaging.html) - [Medical imaging in the browser with the A* Medical Imaging (AMI) toolkit. - Rannou et al. - ESMRMB 2017 (poster)](http://epostersonline.com/esmrmb2017/node/3443) - [Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization - Bernal-Rusiel et al. - Frontiers in Neuroinformatics 2017 (article)](http://journal.frontiersin.org/article/10.3389/fninf.2017.00032/full) ### 2016 - [Volume Visualization Tools for Medical Applications in Ubiquitous Platforms - Arbelaiz et al. - LNICST 2016 (article)](https://link.springer.com/chapter/10.1007/978-3-319-49655-9_54) - [Interoperable communication of quantitative image analysis results using DICOM standard (DICOM4QI) - Fedorov et al. - RSNA 2016 (poster)](https://docs.google.com/presentation/d/16mZbPiXqU7tKTRAcB7bnP1RGybBLqF-O0319raUWYHo/edit#slide=id.p)