Deep superpixel generation and clustering for weakly supervised segmentation of brain tumors in MR images

Training machine learning models to segment tumors and other anomalies in medical images is an important step for developing diagnostic tools but generally requires manually annotated ground truth segmentations, which necessitates significant time and resources. We aim to develop a pipeline that can be trained using readily accessible binary image-level classification labels, to effectively segment regions of interest without requiring ground truth annotations.

This work proposes the use of a deep superpixel generation model and a deep superpixel clustering model trained simultaneously to output weakly supervised brain tumor segmentations. The superpixel generation model's output is selected and clustered together by the superpixel clustering model. Additionally, we train a classifier using binary image-level labels (i.e., labels indicating whether an image contains a tumor), which is used to guide the training by localizing undersegmented seeds as a loss term. The proposed simultaneous use of superpixel generation and clustering models, and the guided localization approach allow for the output weakly supervised tumor segmentations to capture contextual information that is propagated to both models during training, resulting in superpixels that specifically contour the tumors. We evaluate the performance of the pipeline using Dice coefficient and 95% Hausdorff distance (HD95) and compare the performance to state-of-the-art baselines. These baselines include the state-of-the-art weakly supervised segmentation method using both seeds and superpixels (CAM-S), and the Segment Anything Model (SAM).

We used 2D slices of magnetic resonance brain scans from the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2020 dataset and labels indicating the presence of tumors to train and evaluate the pipeline. On an external test cohort from the BraTS 2023 dataset, our method achieved a mean Dice coefficient of 0.745 and a mean HD95 of 20.8, outperforming all baselines, including CAM-S and SAM, which resulted in mean Dice coefficients of 0.646 and 0.641, and mean HD95 of 21.2 and 27.3, respectively.

The proposed combination of deep superpixel generation, deep superpixel clustering, and the incorporation of undersegmented seeds as a loss term improves weakly supervised segmentation.