FIESTA: Autoencoders for accurate fiber segmentation in tractography.

White matter bundle segmentation is a cornerstone of modern tractography to study the brain's structural connectivity in domains such as neurological disorders, neurosurgery, and aging. In this study, we present FIESTA (FIbEr Segmentation in Tractography using Autoencoders), a reliable and robust, fully automated, and easily semi-automatically calibrated pipeline based on deep autoencoders that can dissect and fully populate white matter bundles. This pipeline is built upon previous works that demonstrated how autoencoders can be used successfully for streamline filtering, bundle segmentation, and streamline generation in tractography. Our proposed method improves bundle segmentation coverage by recovering hard-to-track bundles with generative sampling through the latent space seeding of the subject bundle and the atlas bundle. A latent space of streamlines is learned using autoencoder-based modeling combined with contrastive learning. Using an atlas of bundles in standard space (MNI), our proposed method segments new tractograms using the autoencoder latent distance between each tractogram streamline and its closest neighbor bundle in the atlas of bundles. Intra-subject bundle reliability is improved by recovering hard-to-track streamlines, using the autoencoder to generate new streamlines that increase the spatial coverage of each bundle while remaining anatomically correct. Results show that our method is more reliable than state-of-the-art automated virtual dissection methods such as RecoBundles, RecoBundlesX, TractSeg, White Matter Analysis and XTRACT. Our framework allows for the transition from one anatomical bundle definition to another with marginal calibration efforts. Overall, these results show that our framework improves the practicality and usability of current state-of-the-art bundle segmentation framework.

Filtering in tractography using autoencoders (FINTA).

Current brain white matter fiber tracking techniques show a number of problems, including: generating large proportions of streamlines that do not accurately describe the underlying anatomy; extracting streamlines that are not supported by the underlying diffusion signal; and under-representing some fiber populations, among others. In this paper, we describe a novel autoencoder-based learning method to filter streamlines from diffusion MRI tractography, and hence, to obtain more reliable tractograms. Our method, dubbed FINTA (Filtering in Tractography using Autoencoders) uses raw, unlabeled tractograms to train the autoencoder, and to learn a robust representation of brain streamlines. Such an embedding is then used to filter undesired streamline samples using a nearest neighbor algorithm. Our experiments on both synthetic and in vivo human brain diffusion MRI tractography data obtain accuracy scores exceeding the 90% threshold on the test set. Results reveal that FINTA has a superior filtering performance compared to conventional, anatomy-based methods, and the RecoBundles state-of-the-art method. Additionally, we demonstrate that FINTA can be applied to partial tractograms without requiring changes to the framework. We also show that the proposed method generalizes well across different tracking methods and datasets, and shortens significantly the computation time for large (>1 M streamlines) tractograms. Together, this work brings forward a new deep learning framework in tractography based on autoencoders, which offers a flexible and powerful method for white matter filtering and bundling that could enhance tractometry and connectivity analyses.

MIO-TCD: A new benchmark dataset for vehicle classification and localization.

The ability to train on a large dataset of labeled samples is critical to the success of deep learning in many domains. In this paper, we focus on motor vehicle classification and localization from a single video frame and introduce the "MIOvision Traffic Camera Dataset" (MIO-TCD) in this context. MIO-TCD is the largest dataset for motorized traffic analysis to date. It includes 11 traffic object classes such as cars, trucks, buses, motorcycles, bicycles, pedestrians. It contains 786,702 annotated images acquired at different times of the day and different periods of the year by hundreds of traffic surveillance cameras deployed across Canada and the United States. The dataset consists of two parts: a "localization dataset", containing 137,743 full video frames with bounding boxes around traffic objects, and a "classification dataset", containing 648,959 crops of traffic objects from the 11 classes. We also report results from the 2017 CVPR MIO-TCD Challenge, that leveraged this dataset, and compare them with results for state-of-the-art deep learning architectures. These results demonstrate the viability of deep learning methods for vehicle localization and classification from a single video frame in real-life traffic scenarios. The topperforming methods achieve both accuracy and Kappa score above 96% on the classification dataset and mean-average precision of 77% on the localization dataset. We also identify scenarios in which state-of-the-art methods still fail and we suggest avenues to address these challenges. Both the dataset and detailed results are publicly available on-line [1].