BioImage Suite Web -- Browser Package

This is package exports much of functionality in BioImage Suite Web as an npm package for use inside a Browser (or Electron). For more on BioImage Suite Web see:

• The source repository -- https://github.com/bioimagesuiteweb/bisweb
• The actual web application -- https://bioimagesuiteweb.github.io/webapp/

You may also take a look at the examples repository https://github.com/bioimagesuiteweb/examples.

BioImage Suite Web (bisweb) is a web-based medical image analysis suite primarily geared towards Neuroimaging Analysis. We gratefully acknowledge support from the NIH Brain Initiative under grant R24 MH114805 (Papademetris X. and Scheinost D. PIs).

Installation

Simply type:

npm install biswebbrowser

Including in your application's html header

In the header of your html file include: (Replace node_modules with the relative path from your .html file to node_modules)

a. The CSS dependencies (only needed if you will use BioImage Suite Web UI Components)

Either the slightly customized BioImage Suite Web dark bootstrap style (this is bootstrap 3.4.0)

<link rel="stylesheet" type="text/css href="node_modules/biswebbrowser/dist/bootstrap_dark_edited.css">

or a standard light style:

<link rel="stylesheet" type="text/css href="node_modules/biswebbrowser/dist/css/bootstrap.min.css">

b. The external JS dependencies (jQuery 3.3.1, THREE.js 0.100.0, Bootstrap 3.4.0 and the Polymer webcomponents package)

<script src="node_modules/biswebbrowser/dist/webcomponents-lite.js"></script>
<script src="node_modules/biswebbrowser/dist/jquery.min.js"></script>
<script src="node_modules/biswebbrowser/dist/bootstrap.min.js"></script>
<script src="node_modules/biswebbrowser/dist/three.min.js"></script>

c. The BioImage Suite Web Files JS/WASM files

<script src="node_modules/biswebbrowser/dist/libbiswasm_wasm.js"></script>
<script src="node_modules/biswebbrowser/dist/bislib.js"></script>

If you would like (for whatever reason) not to include GPL licensed code, then include the non-GPL WASM code (Apache) script instead of libbiswasm_wasm.js.

<script src="node_modules/bisweb/dist/libbiswasm_nongpl_wasm.js"></script>

Example JS Code

Here is some sample js code that uses this:

const bisweb=window.bioimagesuiteweb;

window.onload = function() {

    console.log('Bisweb=',bisweb);

    let img=new bisweb.BisWebImage();

    img.load("https://bioimagesuiteweb.github.io/unstableapp/images/MNI_T1_2mm_stripped_ras.nii.gz").then( () => {
        console.log('Image Loaded = ',img.getDescription());

        let mod=bisweb.createModule("resampleImage");
         console.log('Module created=',mod);

         mod.execute( { "input" : img   }, { "xsp"  : 2.0, "ysp" : 3.0, "zsp" : 4.0
                                  }).then( () => {
                                      let out=mod.getOutputObject("output");
                                      console.log('OutImage = ',out.getDescription());
                                      out.save();
                                  });
    });
 };

For more, see the ./dist/exportexample.html that is part of this npm package or the examples repository linked to above.

Using with Webpack

If you are using Webpack in your own application and you would like to bundle bioimagesuite web within your bundle you will need to:

1. Add the following to the externals part of your webpack configuration

    externals: {
        "jquery": "jQuery",
        "jQuery": "jQuery",
        "THREE": "THREE", 
    },
       

2. Include bioimagesuiteweb using require (instead of the script tag), e.g.

    const bioimagesuiteweb=require('biswebbrowser');

3. You will still need to include the following in the heaeder of your webpage -- the only file not needed is bislib.js.

    <script src="node_modules/biswebbrowser/dist/webcomponents-lite.js"></script>
    <script src="node_modules/biswebbrowser/dist/jquery.min.js"></script>
    <script src="node_modules/biswebbrowser/dist/bootstrap.min.js"></script>
    <script src="node_modules/biswebbrowser/dist/three.min.js"></script>
    <script src="node_modules/biswebbrowser/dist/libbiswasm_wasm.js"></script>

Electron

If you are planning to use this code in an electron application, you will need to include the file ./electron/electronpreload.js in your electron preload script for as to allow access to lower level code.

You will also need to install the node.js pre-requisites specified in ./electron/electrondependencies.json appropriately. The tensorflow package (tfjs-node) is optional.

Regression Testing

I assume that you have some form of web server running. If you do not, you can use simple-server. See: https://www.npmjs.com/package/simple-server more information.

Once you have a server up and running, simply navigate to one of the following:

• node_modules/biswebbrowser/dist/biswebtest.html -- module tests

• node_modules/biswebbrowser/dist/biswebdisplaytest.html -- display tests I

• node_modules/biswebbrowser/dist/biswebdisplaytest2.html -- display tests II

For more info on the tests see https://bioimagesuiteweb.github.io/bisweb-manual/biswebtest.html.