$productCollection = $category->getProductCollection();

//product stock status is 1 that's in stock

$productCollection->getSelect()->joinInner(array('pStock'=>'cataloginventory_stock_status'),"pStock.product_id=e.entity_id and pStock.stock_status=1","pStock.stock_status")
                                               ->columns('visibility','cat_index');

//product status is enabled and is not  unvisibility
  $productCollection->addAttributeToFilter("status",array("eq"=>1))
                                  ->addAttributeToFilter("visibility",array('neq'=>1));
 $count = $productCollection->count();