A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation

Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components. In this paper, we propose a convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate that the autoencoder can be used for efficient and coarse characterization of features of macromolecular complexes and surfaces, such as membranes. In addition, the autoencoder can be used to detect non-cellular features related to sample preparation and data collection, such as carbon edges from the grid and tomogram boundaries. The autoencoder is also able to detect patterns that may indicate spatial interactions between cellular components. Furthermore, we demonstrate that our autoencoder can be used for weakly supervised semantic segmentation of cellular components, requiring a very small amount of manual annotation.Comment: Accepted by Journal of Structural Biolog

Towards Accurate Camera Geopositioning by Image Matching

In this work, we present a camera geopositioning system based on matching a query image against a database with panoramic images. For matching, our system uses memory vectors aggregated from global image descriptors based on convolutional features to facilitate fast searching in the database. To speed up searching, a clustering algorithm is used to balance geographical positioning and computation time. We refine the obtained position from the query image using a new outlier removal algorithm. The matching of the query image is obtained with a recall@5 larger than 90% for panorama-to-panorama matching. We cluster available panoramas from geographically adjacent locations into a single compact representation and observe computational gains of approximately 50% at the cost of only a small (approximately 3%) recall loss. Finally, we present a coordinate estimation algorithm that reduces the median geopositioning error by up to 20%