CountPost WordPress Custom Taxonomy

I do not know exactly what you mean, but I think you need something like this?

$categories = get_terms( array( 'taxonomy' => 'category' ) );
if ( $categories ) { 
   $output="";
   foreach( $categories as $category ) {
      $output .= '<li title="' . __( 'View all', 'themename' ) . ' ' . $category->count . ' ' . __( 'posts in', 'themename' ) . ' ' . $category->name . '">' . $category->name . ' ' . $separator . '</li>';
   }
   echo trim( $output, $separator );
}