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https://github.com/fnndsc/ami
AMI Medical Imaging (AMI) JS ToolKit
https://github.com/fnndsc/ami
ami dicom dicom-images fs javascript medical nifti nifti-format nrrd stl threejs trk volume-rendering vtk webgl xtk
Last synced: about 1 month ago
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AMI Medical Imaging (AMI) JS ToolKit
- Host: GitHub
- URL: https://github.com/fnndsc/ami
- Owner: FNNDSC
- License: mit
- Created: 2015-02-05T09:37:09.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2022-12-10T01:30:36.000Z (almost 2 years ago)
- Last Synced: 2024-10-11T14:02:09.903Z (about 1 month ago)
- Topics: ami, dicom, dicom-images, fs, javascript, medical, nifti, nifti-format, nrrd, stl, threejs, trk, volume-rendering, vtk, webgl, xtk
- Language: JavaScript
- Homepage: https://fnndsc.github.io/ami/#viewers_upload
- Size: 159 MB
- Stars: 716
- Watchers: 67
- Forks: 213
- Open Issues: 143
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
----------
### 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
Load DICOM Data and get a nice Series/Stack/Frame structure.
Look at the data we loaded in 3D.
Add a mesh to the scene.
Look at the data in 2D.
Overlays on top of you data.
Lesson 05: TRK
TRK - coming soon.
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](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
```
### 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
#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
#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)
