<ul id="tree" class="bonsai">
...
//some jquery-bonsai staff
...
<ul class="bonsai" style="height: auto;">
<li class="has-children expanded">
    <div class="thumb"></div>
    <input type="checkbox" name="undefined" id="bonsai-checkbox-1" value="">
    <label for="bonsai-checkbox-1">calibre</label>
    <ul class="bonsai" style="height: auto;">
            <li onclick="getPath(this.id)" class="bonsai-tree" data-name="bonsai-tree" data-value="CLN16FFP_10M_2Xa1Xd3Xe2Y1Z_002.11b.encrypt">
            <div class="thumb"></div>
            <input type="checkbox" name="bonsai-tree" id="bonsai-checkbox-2" value="CLN16FFP_10M_2Xa1Xd3Xe2Y1Z_002.11b.encrypt">
            <label for="bonsai-checkbox-2">CLN16FFP_10M_2Xa1Xd3Xe2Y1Z_002.11b.encrypt</label>
        </li>
...
...

}
    })
}
ul.html += '</ul></li>' + "n";

$('#tree').html(tree_out.html);

$('#tree').bonsai({
    // expandAll: true,
    checkboxes: true, // depends on jquery.qubit plugin
    createInputs: 'checkbox' // takes values from data-name and data-value, and data-name is inherited
});
$('#tree').bonsai('update');