When creating a custom Wordpress theme with Bootstrap, it took me forever for it to play nicely with the Isotope plugin for image filtering. Wanted to share in hopes it helps others.

functions for custom portfolio type and taxonomies

<!--
The function code enables a custom Portfolio type in the Wordpress admin section. Projects added here and their categories 
will appear where the portfolio code is placed. You will need to register the Isotope plugin in order for it to function properly.
Isotope website: http://isotope.metafizzy.co/
-->

<?php

  wp_register_script( 'plugins', get_template_directory_uri() . '/assets/js/build/plugins.min.js', array( 'jquery' ), '', all );
	wp_enqueue_script( 'plugins');
		
	if ( function_exists( 'add_image_size' ) ) {
		add_image_size( 'portfolio', 350, 350 );
	}
	
	add_action('init', 'create_portfolio');
	function create_portfolio() {
		$labels = array(
			'name' 				=> _x('Portfolio', 'post type general name'),
			'singular_name' 		=> _x('Portfolio', 'post type singular name'),
			'add_new' 			=> _x('Add New', 'portfolio'),
			'add_new_item' 			=> __('Add New Portfolio Item'),
			'edit_item' 			=> __('Edit Item'),
			'new_item' 			=> __('New Item'),
			'view_item' 			=> __('View Item'),
			'search_items' 			=> __('Search Items'),
			'not_found' 			=> __('No items found'),
			'not_found_in_trash' 		=> __('No items found in Trash'),
			'parent_item_colon' 		=> ''
		);
		$args = array(
			'labels' 			=> $labels,
			'public' 			=> true,
			'show_ui' 			=> true,
			'query_var' 			=> true,
			'rewrite' 			=> true,
			'capability_type' 		=> 'post',
			'hierarchical' 			=> false,
			'menu_position' 		=> null,
			'menu_icon'			=> 'dashicons-portfolio',
			'supports' 			=> array('title', 'editor', 'thumbnail', 'comments')
		);
		register_post_type('portfolio', $args);
	}
		register_taxonomy( "portfolio-categories",
		array( "portfolio" ),
		array( "hierarchical" 				=> true,
					"labels" 		=> array('name'=>"Creative Fields", 'add_new_item'=>'Add New Field'),
					"singular_label" 	=> __( "Field" ),
					"rewrite" 		=> array( 'slug' => 'fields',
					'with_front' 		=> false)
				)
		);

	function portfolio_icons() {
		?>
		<style type="text/css" media="screen">
			#menu-posts-portfolio .wp-menu-image {
				background: url(<?php bloginfo('template_url') ?>/assets/Pages_Add.png) no-repeat 6px -17px !important;
			}
			#menu-posts-portfolio:hover .wp-menu-image,
			#menu-posts-portfolio.wp-has-current-submenu .wp-menu-image {
				background-position: 6px 7px !important;
			}
		</style>
	<?php }

?>

Wordpress portfolio template with Isotope and Bootstrap

<!--PHP file for adding a basic template portfolio page for Wordpress themes using the Bootstrap framework.-->

<?php
/*
Template Name: Portfolio
*/
?>

<?php get_header(); ?>

<div class="page-header">
<div class="container">
  <h1>Portfolio</h1>
  
	<div class="portfolio-filter" class="row">
		<ul class="filter">
			<?php
				$terms = get_terms('portfolio-categories');
				$count = count($terms);
					echo '<li><a class="active" href="#" data-filter="*">All</a></li>';
				if ( $count > 0 ) {
					foreach ( $terms as $term ) {
						$termname = strtolower($term->name);
						$termname = str_replace(' ', '-', $termname);
						echo '<li><a href="#" data-filter=".'.$termname.'">'.$term->name.'</a><li>';
					}
				}
			?>
		</ul>
	</div>
</div>
</div>
<div class="portfolio">
<div class="row">
	<div class="container">
		<div class="isotope">
			<ul class="projects">

				<?php
					$args = array( 'post_type' => 'portfolio', 'posts_per_page' => -1 );
					$wp_query_portfolio = new WP_Query( $args );
						while( $wp_query_portfolio->have_posts() ) : $wp_query_portfolio->the_post();

					$terms = get_the_terms( $post->ID, 'portfolio-categories' );
						if( $terms && ! is_wp_error( $terms ) ) :
							$links = array();
							foreach ( $terms as $term ) {
								$links[] = $term->name;
							}

							$tax_links = join( " ", str_replace(' ', '-', $links));
							$tax = strtolower($tax_links);
						else :
							$tax = '';
						endif;

						echo '<li class="project col-xs-12 col-sm-3 col-md-3 all '. $tax .'">';
						echo '<a class="wrap-overlay" href="'. get_permalink() .'">';
						echo the_post_thumbnail('portfolio');
						echo '<div class="overlay">';
						echo '</div>';
						echo '</a>';
						echo '<a class="project-name" href="'. get_permalink() .'">';
						echo '<p>'. get_the_title() .'</p>'; 
						echo '<p>'. ucfirst($tax) .'</p>';
						echo '</a>';
						echo '</li>';

				endwhile; ?>
				
			</ul>
		</div>
	</div>
</div>
</div>

<?php get_footer(); ?>