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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

$3

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);
`

$3

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.

$3

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

$3

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




$3

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.

$3

Remove the neuron from memory and stop displaying it.

#### Arguments

* name [string]: The name used when loading the neuron.

$3

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


Scientific Computing

Janelia Research Campus

Howard Hughes Medical Institute