Ultrasound Localization Microscopy can resolve the microvascular bed down to a few micrometers. To achieve such performance microbubble contrast agents must perfuse the entire microvascular network. Microbubbles are then located individually and tracked over time to sample individual vessels, typically over hundreds of thousands of images. To overcome the fundamental limit of diffraction and achieve a dense reconstruction of the network, low microbubble concentrations must be used, which lead to acquisitions lasting several minutes. Conventional processing pipelines are currently unable to deal with interference from multiple nearby microbubbles, further reducing achievable concentrations. This work overcomes this problem by proposing a Deep Learning approach to recover dense vascular networks from ultrasound acquisitions with high microbubble concentrations. A realistic mouse brain microvascular network, segmented from 2-photon microscopy, was used to train a three-dimensional convolutional neural network based on a V-net architecture. Ultrasound data sets from multiple microbubbles flowing through the microvascular network were simulated and used as ground truth to train the 3D CNN to track microbubbles. The 3D-CNN approach was validated in silico using a subset of the data and in vivo on a rat brain acquisition. In silico, the CNN reconstructed vascular networks with higher precision (81%) than a conventional ULM framework (70%). In vivo, the CNN could resolve micro vessels as small as 10 𝝁𝒎 with an increase in resolution when compared against a conventional approach.

Image segmentation is one of the most popular problems in medical image analysis. Recently, with the success of deep neural networks, these powerful methods provide state of the art performance on various segmentation tasks. However, one of the main challenges relies on the high number of annotations that they need to be trained, which is crucial in medical applications. In this paper, we propose an unsupervised method based on deep learning for the segmentation of kidney grafts. Our method is composed of two different stages, the detection of the area of interest and the segmentation model that is able, through an iterative process, to provide accurate kidney draft segmentation without the need for annotations. The proposed framework works in the 3D space to explore all the available information and extract meaningful representations from Dynamic Contrast-Enhanced and T2 MRI sequences. Our method reports a dice of 89.8 ± 3.1%, Hausdorff distance at percentile 95% of 5.8±0.41mm and percentage of kidney volume difference of 5.9 ± 5.7% on a test dataset of 29 patients subject to a kidney transplant.