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Background: Deep learning (DL) has shown promising results in improving atrial fibrillation (AF) detection algorithms. However, these models are often criticized because of their "black box" nature. Aim: To develop a morphology based DL model to discriminate AF from sinus rhythm (SR), and to visualize which parts of the ECG are used by the model to derive to the right classification. Methods: We pre-processed raw data of 1469 ECGs in AF or SR, of patients with a history AF. Input data was generated by normalizing all single cycles (SC) of one ECG lead to SC-ECG samples by 1) centralizing the R wave or 2) scaling from R-to-R wave. Different DL models were trained by splitting the data in a training, validation and test set. By using a DL based heat mapping technique we visualized those areas of the ECG used by the classifier to come to the correct classification.Results: The DL model with the best performance was a feedforward neural network trained by SC-ECG samples on a R-to-R wave basis of lead II, resulting in an accuracy of 0.96 and F1-score of 0.94. The onset of the QRS complex proved to be the most relevant area for the model to discriminate AF from SR. Conclusion:The morphology based DL model developed in this study was able to discriminate AF from SR with a very high accuracy. DL model visualization may help clinicians gain insights into which (unrecognized) ECG features are most sensitive to discriminate AF from SR.