Adaptive optics scanning laser ophthalmoscopy (AOSLO) provides real-time retinal images with high resolution down to 2 $\mu m$. This technique enables detection of the morphologies of individual microaneurysms (MAs), which are one of the earliest signs of diabetic retinopathy (DR), a frequent complication of diabetes that can lead to visual impairment and blindness. In contrast to previous automatic models developed for MA detection on standard fundus photographs, currently there is no high throughput image protocol available for automatic analysis of AOSLO photographs. To address this urgency, we introduce AOSLO-net, a deep neural network framework with customized training policy, including preprocessing, data augmentation and transfer learning, to automatically segment MAs from AOSLO images. We evaluate the performance of AOSLO-net using 87 DR AOSLO images demonstrating very accurate MA detection and segmentation, leading to correct MA morphological classification, while outperforming the state-of-the-art both in accuracy and cost.