A deep learning based tool for automatic brain extraction from functional magnetic resonance images in rodents

Removing skull artifacts from functional magnetic images (fMRI) is a well understood and frequently encountered problem. Because the fMRI field has grown mostly due to human studies, many new tools were developed to handle human data. Nonetheless, these tools are not equally useful to handle the data derived from animal studies, especially from rodents. This represents a major problem to the field because rodent studies generate larger datasets from larger populations, which implies that preprocessing these images manually to remove the skull becomes a bottleneck in the data analysis pipeline. In this study, we address this problem by implementing a neural network based method that uses a U-Net architecture to segment the brain area into a mask and removing the skull and other tissues from the image. We demonstrate several strategies to speed up the process of generating the training dataset using watershedding and several strategies for data augmentation that allowed to train faster the U-Net to perform the segmentation. Finally, we deployed the trained network freely available.

DeepTEGINN: Deep Learning Based Tools to Extract Graphs from Images of Neural Networks

In the brain, the structure of a network of neurons defines how these neurons implement the computations that underlie the mind and the behavior of animals and humans. Provided that we can describe the network of neurons as a graph, we can employ methods from graph theory to investigate its structure or use cellular automata to mathematically assess its function. Although, software for the analysis of graphs and cellular automata are widely available. Graph extraction from the image of networks of brain cells remains difficult. Nervous tissue is heterogeneous, and differences in anatomy may reflect relevant differences in function. Here we introduce a deep learning based toolbox to extracts graphs from images of brain tissue. This toolbox provides an easy-to-use framework allowing system neuroscientists to generate graphs based on images of brain tissue by combining methods from image processing, deep learning, and graph theory. The goals are to simplify the training and usage of deep learning methods for computer vision and facilitate its integration into graph extraction pipelines. In this way, the toolbox provides an alternative to the required laborious manual process of tracing, sorting and classifying. We expect to democratize the machine learning methods to a wider community of users beyond the computer vision experts and improve the time-efficiency of graph extraction from large brain image datasets, which may lead to further understanding of the human mind.