/SharkViewer

SharkViewer is a web-based viewer for SWC neuron files. It is written entirely in JavaScript using Three.js.

Primary LanguageJavaScriptOtherNOASSERTION

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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
npm install
  1. Start up a test server
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
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.
var s = new sharkViewer({ dom_element: 'container' });
  1. Initialize the SharkViewer
s.init();
  1. Animate the SharkViewer
s.animate();
  1. load in a neuron swc file.
const swcJSON = swcParser(swcText);
s.loadNeuron('neuron_name', '#ff0000', swcJSON);

AS A LIBRARY

  1. download this repository
  2. copy lib/shark_viewer.js and lib/three.min.js into your project
  3. Load the javascript files into your page
<script src="three.min.js"></script>
<script src="shark_viewer.js"></script>
  1. Create a new SharkViewer object. At a minimum you need to give it a DOM element to attach a canvas to.
var s = new sharkViewer.default({ swc: swc, dom_element: 'container' });
  1. Initialize the SharkViewer
s.init();
  1. Animate the SharkViewer
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.
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

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.
swc json object: {
    id : {
        type: <type number of node (string)>,
        x: <x position of node (float)>,
        y: <y position of node (float)>,
        z: <z position of node (float)>,
        parent: <id number of node parent (-1 if no parent)>,
        radius: <radius of node (float)>,
    }
}
  • 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 (weaverc10@janelia.hhmi.org) and Christopher Bruns (brunsc@janelia.hhmi.org)

Contributors

  • Patrick Edson
  • Jody Clements
  • Phillip Hubbard

Janelia Research Campus

Scientific Computing

Janelia Research Campus

Howard Hughes Medical Institute