To identify autoimmune diseases in humans, analysis of HEp-2 staining patterns at cell level is the gold standard for clinical practice research communities. An automated procedure is a complicated task due to variations in cell densities, sizes, shapes and patterns, overfitting of features, large-scale data volume, stained cells and poor quality of images. Several machine learning methods that analyse and classify HEp-2 cell microscope images currently exist. However, accuracy is still not at the level required for medical applications and computer aided diagnosis due to those challenges. The purpose of this work to automate classification procedure of HEp-2 stained cells from microscopic images and improve the accuracy of computer aided diagnosis. This work proposes Deep Convolutional Neural Networks (DCNNs) technique to classify HEp-2 cell patterns at cell level into six classes based on employing the level-set method via edge detection technique to segment HEp-2 cell shape. The DCNNs are designed to identify cell-shape and fundamental distance features related with HEp-2 cell types. This paper is investigated the effectiveness of our proposed method over benchmarked dataset. The result shows that the proposed method is highly superior comparing with other methods in benchmarked dataset and state-of-the-art methods. The result demonstrates that the proposed method has an excellent adaptability across variations in cell densities, sizes, shapes and patterns, overfitting features, large-scale data volume, and stained cells under different lab environments. The accurate classification of HEp-2 staining pattern at cell level helps increasing the accuracy of computer aided diagnosis for diagnosis process in the future.