Systematic Clinical Evaluation of A Deep Learning Method for Medical Image Segmentation: Radiosurgery Application

We systematically evaluate a Deep Learning (DL) method in a 3D medical image segmentation task. Our segmentation method is integrated into the radiosurgery treatment process and directly impacts the clinical workflow. With our method, we address the relative drawbacks of manual segmentation: high inter-rater contouring variability and high time consumption of the contouring process. The main extension over the existing evaluations is the careful and detailed analysis that could be further generalized on other medical image segmentation tasks. Firstly, we analyze the changes in the inter-rater detection agreement. We show that the segmentation model reduces the ratio of detection disagreements from 0.162 to 0.085 (p < 0.05). Secondly, we show that the model improves the inter-rater contouring agreement from 0.845 to 0.871 surface Dice Score (p < 0.05). Thirdly, we show that the model accelerates the delineation process in between 1.6 and 2.0 times (p < 0.05). Finally, we design the setup of the clinical experiment to either exclude or estimate the evaluation biases, thus preserve the significance of the results. Besides the clinical evaluation, we also summarize the intuitions and practical ideas for building an efficient DL-based model for 3D medical image segmentation.

Universal Loss Reweighting to Balance Lesion Size Inequality in 3D Medical Image Segmentation

Target imbalance affects the performance of recent deep learning methods in many medical image segmentation tasks. It is a twofold problem: class imbalance - positive class (lesion) size compared to negative class (non-lesion) size; lesion size imbalance - large lesions overshadows small ones (in the case of multiple lesions per image). While the former was addressed in multiple works, the latter lacks investigation. We propose a loss reweighting approach to increase the ability of the network to detect small lesions. During the learning process, we assign a weight to every image voxel. The assigned weights are inversely proportional to the lesion volume, thus smaller lesions get larger weights. We report the benefit from our method for well-known loss functions, including Dice Loss, Focal Loss, and Asymmetric Similarity Loss. Additionally, we compare our results with other reweighting techniques: Weighted Cross-Entropy and Generalized Dice Loss. Our experiments show that inverse weighting considerably increases the detection quality, while preserves the delineation quality on a state-of-the-art level. We publish a complete experimental pipeline for two publicly available datasets of CT images: LiTS and LUNA16 (https://github.com/neuro-ml/inverse_weighting). We also show results on a private database of MR images for the task of multiple brain metastases delineation.

Deep Learning for Brain Tumor Segmentation in Radiosurgery: Prospective Clinical Evaluation

Stereotactic radiosurgery is a minimally-invasive treatment option for a large number of patients with intracranial tumors. As part of the therapy treatment, accurate delineation of brain tumors is of great importance. However, slice-by-slice manual segmentation on T1c MRI could be time-consuming (especially for multiple metastases) and subjective (especially for meningiomas). In our work, we compared several deep convolutional networks architectures and training procedures and evaluated the best model in a radiation therapy department for three types of brain tumors: meningiomas, schwannomas and multiple brain metastases. The developed semiautomatic segmentation system accelerates the contouring process by 2.2 times on average and increases inter-rater agreement from 92% to 96.5%.

Tumor Delineation For Brain Radiosurgery by a ConvNet and Non-Uniform Patch Generation

Deep learning methods are actively used for brain lesion segmentation. One of the most popular models is DeepMedic, which was developed for segmentation of relatively large lesions like glioma and ischemic stroke. In our work, we consider segmentation of brain tumors appropriate to stereotactic radiosurgery which limits typical lesion sizes. These differences in target volumes lead to a large number of false negatives (especially for small lesions) as well as to an increased number of false positives for DeepMedic. We propose a new patch-sampling procedure to increase network performance for small lesions. We used a 6-year dataset from a stereotactic radiosurgery center. To evaluate our approach, we conducted experiments with the three most frequent brain tumors: metastasis, meningioma, schwannoma. In addition to cross-validation, we estimated quality on a hold-out test set which was collected several years later than the train one. The experimental results show solid improvements in both cases.

Ensembling Neural Networks for Digital Pathology Images Classification and Segmentation

In the last years, neural networks have proven to be a powerful framework for various image analysis problems. However, some application domains have specific limitations. Notably, digital pathology is an example of such fields due to tremendous image sizes and quite limited number of training examples available. In this paper, we adopt state-of-the-art convolutional neural networks (CNN) architectures for digital pathology images analysis. We propose to classify image patches to increase effective sample size and then to apply an ensembling technique to build prediction for the original images. To validate the developed approaches, we conducted experiments with \textit{Breast Cancer Histology Challenge} dataset and obtained 90\% accuracy for the 4-class tissue classification task.