Enamundram Naga Karthik

Enamundram Naga Karthik, Anne Kerbrat, Pierre Labauge et al.

Segmentation of Multiple Sclerosis (MS) lesions is a challenging problem. Several deep-learning-based methods have been proposed in recent years. However, most methods tend to be static, that is, a single model trained on a large, specialized dataset, which does not generalize well. Instead, the model should learn across datasets arriving sequentially from different hospitals by building upon the characteristics of lesions in a continual manner. In this regard, we explore experience replay, a well-known continual learning method, in the context of MS lesion segmentation across multi-contrast data from 8 different hospitals. Our experiments show that replay is able to achieve positive backward transfer and reduce catastrophic forgetting compared to sequential fine-tuning. Furthermore, replay outperforms the multi-domain training, thereby emerging as a promising solution for the segmentation of MS lesions. The code is available at this link: https://github.com/naga-karthik/continual-learning-ms

Enamundram Naga Karthik, Jan Valošek, Lynn Farner et al.

Spinal cord injury (SCI) is a devastating incidence leading to permanent paralysis and loss of sensory-motor functions potentially resulting in the formation of lesions within the spinal cord. Imaging biomarkers obtained from magnetic resonance imaging (MRI) scans can predict the functional recovery of individuals with SCI and help choose the optimal treatment strategy. Currently, most studies employ manual quantification of these MRI-derived biomarkers, which is a subjective and tedious task. In this work, we propose (i) a universal tool for the automatic segmentation of intramedullary SCI lesions, dubbed \texttt{SCIsegV2}, and (ii) a method to automatically compute the width of the tissue bridges from the segmented lesion. Tissue bridges represent the spared spinal tissue adjacent to the lesion, which is associated with functional recovery in SCI patients. The tool was trained and validated on a heterogeneous dataset from 7 sites comprising patients from different SCI phases (acute, sub-acute, and chronic) and etiologies (traumatic SCI, ischemic SCI, and degenerative cervical myelopathy). Tissue bridges quantified automatically did not significantly differ from those computed manually, suggesting that the proposed automatic tool can be used to derive relevant MRI biomarkers. \texttt{SCIsegV2} and the automatic tissue bridges computation are open-source and available in Spinal Cord Toolbox (v6.4 and above) via the \texttt{sct\_deepseg -task seg\_sc\_lesion\_t2w\_sci} and \texttt{sct\_analyze\_lesion} functions, respectively.

Sandrine Bédard, Enamundram Naga Karthik, Charidimos Tsagkas et al.

Spinal cord segmentation is clinically relevant and is notably used to compute spinal cord cross-sectional area (CSA) for the diagnosis and monitoring of cord compression or neurodegenerative diseases such as multiple sclerosis. While several semi and automatic methods exist, one key limitation remains: the segmentation depends on the MRI contrast, resulting in different CSA across contrasts. This is partly due to the varying appearance of the boundary between the spinal cord and the cerebrospinal fluid that depends on the sequence and acquisition parameters. This contrast-sensitive CSA adds variability in multi-center studies where protocols can vary, reducing the sensitivity to detect subtle atrophies. Moreover, existing methods enhance the CSA variability by training one model per contrast, while also producing binary masks that do not account for partial volume effects. In this work, we present a deep learning-based method that produces soft segmentations of the spinal cord. Using the Spine Generic Public Database of healthy participants ($\text{n}=267$; $\text{contrasts}=6$), we first generated participant-wise soft ground truth (GT) by averaging the binary segmentations across all 6 contrasts. These soft GT, along with aggressive data augmentation and a regression-based loss function, were used to train a U-Net model for spinal cord segmentation. We evaluated our model against state-of-the-art methods and performed ablation studies involving different loss functions and domain generalization methods. Our results show that using the soft segmentations along with a regression loss function reduces CSA variability ($p < 0.05$, Wilcoxon signed-rank test). The proposed spinal cord segmentation model generalizes better than the state-of-the-art methods amongst unseen datasets, vendors, contrasts, and pathologies (compression, lesions), while accounting for partial volume effects.

Uzay Macar, Enamundram Naga Karthik, Charley Gros et al.

This paper gives a detailed description of the pipelines used for the 2nd edition of the MICCAI 2021 Challenge on Multiple Sclerosis Lesion Segmentation. An overview of the data preprocessing steps applied is provided along with a brief description of the pipelines used, in terms of the architecture and the hyperparameters. Our code for this work can be found at: https://github.com/ivadomed/ms-challenge-2021.

Julia Hindel, Ema Mekic, Enamundram Naga Karthik et al.

Robot-assisted surgeries rely on accurate and real-time scene understanding to safely guide surgical instruments. However, segmentation models trained on static datasets face key limitations when deployed in these dynamic and evolving surgical environments. Class-incremental semantic segmentation (CISS) allows models to continually adapt to new classes while avoiding catastrophic forgetting of prior knowledge, without training on previous data. In this work, we build upon the recently introduced Taxonomy-Oriented Poincaré-regularized Incremental Class Segmentation (TOPICS) approach and propose an enhanced variant, termed TOPICS+, specifically tailored for robust segmentation of surgical scenes. Concretely, we incorporate the Dice loss into the hierarchical loss formulation to handle strong class imbalances, introduce hierarchical pseudo-labeling, and design tailored label taxonomies for robotic surgery environments. We also propose six novel CISS benchmarks designed for robotic surgery environments including multiple incremental steps and several semantic categories to emulate realistic class-incremental settings in surgical environments. In addition, we introduce a refined set of labels with more than 144 classes on the Syn-Mediverse synthetic dataset, hosted online as an evaluation benchmark. We make the code and trained models publicly available at http://topics.cs.uni-freiburg.de.

Karthik E

Efficient and accurate object detection in video and image analysis is one of the major beneficiaries of the advancement in computer vision systems with the help of deep learning. With the aid of deep learning, more powerful tools evolved, which are capable to learn high-level and deeper features and thus can overcome the existing problems in traditional architectures of object detection algorithms. The work in this thesis aims to achieve high accuracy in object detection with good real-time performance. In the area of computer vision, a lot of research is going into the area of detection and processing of visual information, by improving the existing algorithms. The binarized neural network has shown high performance in various vision tasks such as image classification, object detection, and semantic segmentation. The Modified National Institute of Standards and Technology database (MNIST), Canadian Institute for Advanced Research (CIFAR), and Street View House Numbers (SVHN) datasets are used which is implemented using a pre-trained convolutional neural network (CNN) that is 22 layers deep. Supervised learning is used in the work, which classifies the particular dataset with the proper structure of the model. In still images, to improve accuracy, Googlenet is used. The final layer of the Googlenet is replaced with the transfer learning to improve the accuracy of the Googlenet. At the same time, the accuracy in moving images can be maintained by transfer learning techniques. Hardware is the main backbone for any model to obtain faster results with a large number of datasets. Here, Nvidia Jetson Nano is used which is a graphics processing unit (GPU), that can handle a large number of computations in the process of object detection. Results show that the accuracy of objects detected by the transfer learning method is more when compared to the existing methods.