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Get Categories Which are visible in Main Navigation in magento 1.9.

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    $collection = Mage::getResourceModel('catalog/category_collection')
        ->addAttributeToSelect('*')
        ->addAttributeToFilter('is_active', 1) //only active categories
        ->addAttributeToFilter('include_in_menu', 1); //only categories included in menu


   foreach ($collection as $category) {

   }

Used this answer: https://magento.stackexchange.com/a/19272/18764

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<?php
    $rootcatId= Mage::app()->getStore()->getRootCategoryId();
    $categories = Mage::getModel('catalog/category')->getCategories($rootcatId);
    function  get_categories($categories) {
        $array= '<ul>';
        foreach($categories as $category) {
            $cat = Mage::getModel('catalog/category')->load($category->getId());
            $count = $cat->getProductCount();
            $array .= '<li>'.
            '<a href="' . Mage::getUrl($cat->getUrlPath()). '">' .
                      $category->getName() . "(".$count.")</a>\n";
            if($category->hasChildren()) {
                $children = Mage::getModel('catalog/category')->getCategories($category->getId());
                 $array .=  get_categories($children);
                }
            $array .= '</li>';
        }
        return  $array . '</ul>';
    }
    echo get_categories($categories); 
?>

You will get all the categories and child categories with product quantity which are included in main navigation. Hope, it will be help

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