https://github.com/janeliascicomp/sharkviewer
SharkViewer is a web-based viewer for SWC neuron files. It is written entirely in JavaScript using Three.js.
https://github.com/janeliascicomp/sharkviewer
Last synced: 9 months ago
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SharkViewer is a web-based viewer for SWC neuron files. It is written entirely in JavaScript using Three.js.
- Host: GitHub
- URL: https://github.com/janeliascicomp/sharkviewer
- Owner: JaneliaSciComp
- License: other
- Created: 2017-06-02T15:48:51.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2023-01-08T10:55:49.000Z (about 3 years ago)
- Last Synced: 2025-04-10T20:21:20.356Z (12 months ago)
- Language: JavaScript
- Homepage:
- Size: 315 MB
- Stars: 24
- Watchers: 7
- Forks: 11
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# Shark Viewer
## NEW
**09-26-2014** - Synapse Annotations. Load annotations from a separate file with format "x y z\n" for each annotation. You can use annotation\_parser(annotation\_text) to parse it into the format [{'x': x, 'y': y, 'z':z}, {'x': x1, 'y': y1, 'z':z1}, ..., {'x': xn, 'y': yn, 'z':zn}] and load that into the annotation property of SharkViewer.
**08-08-2014** - Three.js loader version: html/js/sharkviewer_loader.js
If you want to use the neuron rendered from SharkViewer in another scene use this version. html/Shark\_Viewer\_Loader\_Version.html shows an example of how to use it.
**06-18-2014** - Serverless SharkViewer! Now the html/Shark\_Viewer.html file allows you to load and view your own SWC files without a server. Simply download the repository and open Shark\_Viewer.html in a browser, then use the form to view your own SWC files.
## DESCRIPTION
SharkViewer is a web-based viewer for SWC neuron files. It is written entirely in JavaScript using Three.js.
To view SWC format guidelines visit: http://research.mssm.edu/cnic/swc.html
## EXAMPLE
http://janeliascicomp.github.io/SharkViewer/
## QUICK START
1. Install the dependencies
```zsh
npm install
```
1. Start up a test server
```zsh
npm run start
```
1. Click 'Choose File' button to load a SWC file.
## USAGE
### AS A MODULE
1. fetch the package
```
npm install @janelia/sharkviewer
```
1. import
```javascript
import SharkViewer, { swcParser } from sharkViewer;
```
1. Create a new SharkViewer object. At a minimum you need to give it a DOM element to attach a canvas to.
```javascript
var s = new sharkViewer({ dom_element: 'container' });
```
1. Initialize the SharkViewer
```javascript
s.init();
```
1. Animate the SharkViewer
```javascript
s.animate();
```
1. load in a neuron swc file.
```javascript
const swcJSON = swcParser(swcText);
s.loadNeuron('neuron_name', '#ff0000', swcJSON);
```
### AS A LIBRARY
1. download this repository
1. copy lib/shark_viewer.js and lib/three.min.js into your project
1. Load the javascript files into your page
```HTML
```
1. Create a new SharkViewer object. At a minimum you need to give it a DOM element to attach a canvas to.
```javascript
var s = new sharkViewer.default({ swc: swc, dom_element: 'container' });
```
1. Initialize the SharkViewer
```javascript
s.init();
```
1. Animate the SharkViewer
```javascript
s.animate();
```
1. Load an SWC file into json. There is a helper function swcParser(swcText) available, or you can write your own to process it server side and load via AJAX.
```javascript
var swcJSON = sharkViewer.swcParser(swcTxt); ;
s.loadNeuron('neuron_name', '#ff0000', swcJSON);
```
lib/index.html shows an example of this setup.
### sharkViewer.default()
Create a new SharkViewer instance to display a collection of neurons.
#### Arguments
* dom_element - html element that will receive the webgl canvas
* *Default*: 'container'
* mode - sphere (full 3-D rendering for nodes and connections, slow), particle (uses particle system to speed rendering and make it look better), or skeleton (no nodes, just connections, very fast)
* *Default*: 'particle'
* show_cones - show cones between cylinders for particle and sphere mode
* *Default*: true;
* colors - color array for display, nodes of type 0 show as first color, etc.
* *Default*:
```
[
0x00be9e,
0x3919cb,
0x7d0bc4,
0xff6700,
0x3eef00,
0xffce00,
0xf50027,
0x606060,
]
```
* metadata - array of javascript objects with labels and type numbers to display as legend (type number matches to type column in swc file) format:
* *Default*: false
* Example:
```
[{"label":"undefined","type":0},{"label":"soma","type":1}]
```
* annotation - array of javascript objects with x, y, z coordinates to display as synapse annotations.
* *Default*: false
* Example:
```
[{'x': x, 'y': y, 'z':z}, {'x': x1, 'y': y1, 'z':z1}, ..., {'x': xn, 'y': yn, 'z':zn}]
```
* annotation_color - color to display annotations
*Default* 0x111111
### sharkViewer.swcParser(swcText)
Parse SWC files into a JSON format for loading into the viewer.
#### Arguments
* **swcText** [string]:
An SWC file based on the format described at [http://research.mssm.edu/cnic/swc.html](http://research.mssm.edu/cnic/swc.html)
### sharkViewer.loadNeuron(name, color, swcJSON, updateCamera)
Load a neuron SWC JSON object into the viewer and center the camera around it.
#### Arguments
* **name** [string]: A simple text string used to identify the object.
Used by other functions to remove or hide it.
* **color** [string]: Hexadecimal string to determine the color of the neuron.
* **swcJSON** [JSON]: JSON string representation of the SWC file. A description of
the expected format is shown below.
```javascript
swc json object: {
id : {
type: ,
x: ,
y: ,
z: ,
parent: ,
radius: ,
}
}
```
* **updateCamera** [boolean]: If false the camera will not center around the newly added object.
### unloadNeuron(name)
Remove the neuron from memory and stop displaying it.
#### Arguments
* **name** [string]: The name used when loading the neuron.
### setNeuronVisible(name, visible)
Show or hide the neuron object, without removing it from the scene.
#### Arguments
* **name** [string]: The name used when loading the neuron.
* **visible** [boolean]: true to show the neuron, false to hide it.
## Author Information
SharkViewer was originally written by Charlotte Weaver () and Christopher Bruns ()
## Contributors
- Patrick Edson
- Jody Clements
- Phillip Hubbard
[](http://www.janelia.org)
[Scientific Computing](http://www.janelia.org/research-resources/computing-resources)
[Janelia Research Campus](http://www.janelia.org)
[Howard Hughes Medical Institute](http://www.hhmi.org)