CALF: A Conditionally Adaptive Loss Function to Mitigate Class-Imbalanced Segmentation

Imbalanced datasets pose a considerable challenge in training deep learning (DL) models for medical diagnostics, particularly for segmentation tasks. Imbalance may be associated with annotation quality limited annotated datasets, rare cases, or small-scale regions of interest (ROIs). These conditions adversely affect model training and performance, leading to segmentation boundaries which deviate from the true ROIs. Traditional loss functions, such as Binary Cross Entropy, replicate annotation biases and limit model generalization. We propose a novel, statistically driven, conditionally adaptive loss function (CALF) tailored to accommodate the conditions of imbalanced datasets in DL training. It employs a data-driven methodology by estimating imbalance severity using statistical methods of skewness and kurtosis, then applies an appropriate transformation to balance the training dataset while preserving data heterogeneity. This transformative approach integrates a multifaceted process, encompassing preprocessing, dataset filtering, and dynamic loss selection to achieve optimal outcomes. We benchmark our method against conventional loss functions using qualitative and quantitative evaluations. Experiments using large-scale open-source datasets (i.e., UPENN-GBM, UCSF, LGG, and BraTS) validate our approach, demonstrating substantial segmentation improvements. Code availability: https://anonymous.4open.science/r/MICCAI-Submission-43F9/.

SMILE-UHURA Challenge -- Small Vessel Segmentation at Mesoscopic Scale from Ultra-High Resolution 7T Magnetic Resonance Angiograms

The human brain receives nutrients and oxygen through an intricate network of blood vessels. Pathology affecting small vessels, at the mesoscopic scale, represents a critical vulnerability within the cerebral blood supply and can lead to severe conditions, such as Cerebral Small Vessel Diseases. The advent of 7 Tesla MRI systems has enabled the acquisition of higher spatial resolution images, making it possible to visualise such vessels in the brain. However, the lack of publicly available annotated datasets has impeded the development of robust, machine learning-driven segmentation algorithms. To address this, the SMILE-UHURA challenge was organised. This challenge, held in conjunction with the ISBI 2023, in Cartagena de Indias, Colombia, aimed to provide a platform for researchers working on related topics. The SMILE-UHURA challenge addresses the gap in publicly available annotated datasets by providing an annotated dataset of Time-of-Flight angiography acquired with 7T MRI. This dataset was created through a combination of automated pre-segmentation and extensive manual refinement. In this manuscript, sixteen submitted methods and two baseline methods are compared both quantitatively and qualitatively on two different datasets: held-out test MRAs from the same dataset as the training data (with labels kept secret) and a separate 7T ToF MRA dataset where both input volumes and labels are kept secret. The results demonstrate that most of the submitted deep learning methods, trained on the provided training dataset, achieved reliable segmentation performance. Dice scores reached up to 0.838 $\pm$ 0.066 and 0.716 $\pm$ 0.125 on the respective datasets, with an average performance of up to 0.804 $\pm$ 0.15.

PyCellMech: A shape-based feature extraction pipeline for use in medical and biological studies

Summary: Medical researchers obtain knowledge about the prevention and treatment of disability and disease using physical measurements and image data. To assist in this endeavor, feature extraction packages are available that are designed to collect data from the image structure. In this study, we aim to augment current works by adding to the current mix of shape-based features. The significance of shape-based features has been explored extensively in research for several decades, but there is no single package available in which all shape-related features can be extracted easily by the researcher. PyCellMech has been crafted to address this gap. The PyCellMech package extracts three classes of shape features, which are classified as one-dimensional, geometric, and polygonal. Future iterations will be expanded to include other feature classes, such as scale-space. Availability and implementation: PyCellMech is freely available at https://github.com/icm-dac/pycellmech.