23 research outputs found
Spinal cord gray matter segmentation using deep dilated convolutions
Gray matter (GM) tissue changes have been associated with a wide range of
neurological disorders and was also recently found relevant as a biomarker for
disability in amyotrophic lateral sclerosis. The ability to automatically
segment the GM is, therefore, an important task for modern studies of the
spinal cord. In this work, we devise a modern, simple and end-to-end fully
automated human spinal cord gray matter segmentation method using Deep
Learning, that works both on in vivo and ex vivo MRI acquisitions. We evaluate
our method against six independently developed methods on a GM segmentation
challenge and report state-of-the-art results in 8 out of 10 different
evaluation metrics as well as major network parameter reduction when compared
to the traditional medical imaging architectures such as U-Nets.Comment: 13 pages, 8 figure
Unsupervised domain adaptation for medical imaging segmentation with self-ensembling
Recent advances in deep learning methods have come to define the
state-of-the-art for many medical imaging applications, surpassing even human
judgment in several tasks. Those models, however, when trained to reduce the
empirical risk on a single domain, fail to generalize when applied to other
domains, a very common scenario in medical imaging due to the variability of
images and anatomical structures, even across the same imaging modality. In
this work, we extend the method of unsupervised domain adaptation using
self-ensembling for the semantic segmentation task and explore multiple facets
of the method on a small and realistic publicly-available magnetic resonance
(MRI) dataset. Through an extensive evaluation, we show that self-ensembling
can indeed improve the generalization of the models even when using a small
amount of unlabelled data.Comment: 15 pages, 9 figure
Safe Real-World Autonomous Driving by Learning to Predict and Plan with a Mixture of Experts
The goal of autonomous vehicles is to navigate public roads safely and
comfortably. To enforce safety, traditional planning approaches rely on
handcrafted rules to generate trajectories. Machine learning-based systems, on
the other hand, scale with data and are able to learn more complex behaviors.
However, they often ignore that agents and self-driving vehicle trajectory
distributions can be leveraged to improve safety. In this paper, we propose
modeling a distribution over multiple future trajectories for both the
self-driving vehicle and other road agents, using a unified neural network
architecture for prediction and planning. During inference, we select the
planning trajectory that minimizes a cost taking into account safety and the
predicted probabilities. Our approach does not depend on any rule-based
planners for trajectory generation or optimization, improves with more training
data and is simple to implement. We extensively evaluate our method through a
realistic simulator and show that the predicted trajectory distribution
corresponds to different driving profiles. We also successfully deploy it on a
self-driving vehicle on urban public roads, confirming that it drives safely
without compromising comfort. The code for training and testing our model on a
public prediction dataset and the video of the road test are available at
https://woven.mobi/safepathne
Histology-informed automatic parcellation of white matter tracts in the rat spinal cord
The white matter is organized into “tracts” or “bundles,” which connect different parts of the central nervous system. Knowing where these tracts are located in each individual is important for understanding the cause of potential sensorial, motor or cognitive deficits and for developing appropriate treatments. Traditionally, tracts are found using tracer injection, which is a difficult, slow and poorly scalable technique. However, axon populations from a given tract exhibit specific characteristics in terms of morphometrics and myelination. Hence, the delineation of tracts could, in principle, be done based on their morphometry. The objective of this study was to generate automatic parcellation of the rat spinal white matter tracts using the manifold information from scanning electron microscopy images of the entire spinal cord. The axon morphometrics (axon density, axon diameter, myelin thickness and g-ratio) were computed pixelwise following automatic axon segmentation using AxonSeg. The parcellation was based on an agglomerative clustering algorithm to group the tracts. Results show that axon morphometrics provide sufficient information to automatically identify some white matter tracts in the spinal cord, however, not all tracts were correctly identified. Future developments of microstructure quantitative MRI even bring hope for a personalized clustering of white matter tracts in each individual patient. The generated atlas and the associated code can be found at https://github.com/neuropoly/tract-clustering
Data_Sheet_1_Histology-informed automatic parcellation of white matter tracts in the rat spinal cord.PDF
The white matter is organized into “tracts” or “bundles,” which connect different parts of the central nervous system. Knowing where these tracts are located in each individual is important for understanding the cause of potential sensorial, motor or cognitive deficits and for developing appropriate treatments. Traditionally, tracts are found using tracer injection, which is a difficult, slow and poorly scalable technique. However, axon populations from a given tract exhibit specific characteristics in terms of morphometrics and myelination. Hence, the delineation of tracts could, in principle, be done based on their morphometry. The objective of this study was to generate automatic parcellation of the rat spinal white matter tracts using the manifold information from scanning electron microscopy images of the entire spinal cord. The axon morphometrics (axon density, axon diameter, myelin thickness and g-ratio) were computed pixelwise following automatic axon segmentation using AxonSeg. The parcellation was based on an agglomerative clustering algorithm to group the tracts. Results show that axon morphometrics provide sufficient information to automatically identify some white matter tracts in the spinal cord, however, not all tracts were correctly identified. Future developments of microstructure quantitative MRI even bring hope for a personalized clustering of white matter tracts in each individual patient. The generated atlas and the associated code can be found at https://github.com/neuropoly/tract-clustering.</p