Boosting Skull-Stripping Performance for Pediatric Brain Images

Skull-stripping is the removal of background and non-brain anatomical features from brain images. While many skull-stripping tools exist, few target pediatric populations. With the emergence of multi-institutional pediatric data acquisition efforts to broaden the understanding of perinatal brain development, it is essential to develop robust and well-tested tools ready for the relevant data processing. However, the broad range of neuroanatomical variation in the developing brain, combined with additional challenges such as high motion levels, as well as shoulder and chest signal in the images, leaves many adult-specific tools ill-suited for pediatric skull-stripping. Building on an existing framework for robust and accurate skull-stripping, we propose developmental SynthStrip (d-SynthStrip), a skull-stripping model tailored to pediatric images. This framework exposes networks to highly variable images synthesized from label maps. Our model substantially outperforms pediatric baselines across scan types and age cohorts. In addition, the <1-minute runtime of our tool compares favorably to the fastest baselines. We distribute our model at https://w3id.org/synthstrip.

Tyche: Stochastic In-Context Learning for Medical Image Segmentation

Existing learning-based solutions to medical image segmentation have two important shortcomings. First, for most new segmentation task, a new model has to be trained or fine-tuned. This requires extensive resources and machine learning expertise, and is therefore often infeasible for medical researchers and clinicians. Second, most existing segmentation methods produce a single deterministic segmentation mask for a given image. In practice however, there is often considerable uncertainty about what constitutes the correct segmentation, and different expert annotators will often segment the same image differently. We tackle both of these problems with Tyche, a model that uses a context set to generate stochastic predictions for previously unseen tasks without the need to retrain. Tyche differs from other in-context segmentation methods in two important ways. (1) We introduce a novel convolution block architecture that enables interactions among predictions. (2) We introduce in-context test-time augmentation, a new mechanism to provide prediction stochasticity. When combined with appropriate model design and loss functions, Tyche can predict a set of plausible diverse segmentation candidates for new or unseen medical images and segmentation tasks without the need to retrain.

ScribblePrompt: Fast and Flexible Interactive Segmentation for Any Medical Image

Semantic medical image segmentation is a crucial part of both scientific research and clinical care. With enough labelled data, deep learning models can be trained to accurately automate specific medical image segmentation tasks. However, manually segmenting images to create training data is highly labor intensive. In this paper, we present ScribblePrompt, an interactive segmentation framework for medical imaging that enables human annotators to segment unseen structures using scribbles, clicks, and bounding boxes. Scribbles are an intuitive and effective form of user interaction for complex tasks, however most existing methods focus on click-based interactions. We introduce algorithms for simulating realistic scribbles that enable training models that are amenable to multiple types of interaction. To achieve generalization to new tasks, we train on a diverse collection of 65 open-access biomedical datasets -- using both real and synthetic labels. We test ScribblePrompt on multiple network architectures and unseen datasets, and demonstrate that it can be used in real-time on a single CPU. We evaluate ScribblePrompt using manually-collected scribbles, simulated interactions, and a user study. ScribblePrompt outperforms existing methods in all our evaluations. In the user study, ScribblePrompt reduced annotation time by 28% while improving Dice by 15% compared to existing methods. We showcase ScribblePrompt in an online demo and provide code at https://scribbleprompt.csail.mit.edu

GIST: Generating Image-Specific Text for Fine-grained Object Classification

Recent vision-language models outperform vision-only models on many image classification tasks. However, because of the absence of paired text/image descriptions, it remains difficult to fine-tune these models for fine-grained image classification. In this work, we propose a method, GIST, for generating image-specific fine-grained text descriptions from image-only datasets, and show that these text descriptions can be used to improve classification. Key parts of our method include 1. prompting a pretrained large language model with domain-specific prompts to generate diverse fine-grained text descriptions for each class and 2. using a pretrained vision-language model to match each image to label-preserving text descriptions that capture relevant visual features in the image. We demonstrate the utility of GIST by fine-tuning vision-language models on the image-and-generated-text pairs to learn an aligned vision-language representation space for improved classification. We evaluate our learned representation space in full-shot and few-shot scenarios across four diverse fine-grained classification datasets, each from a different domain. Our method achieves an average improvement of $4.1\%$ in accuracy over CLIP linear probes and an average of $1.1\%$ improvement in accuracy over the previous state-of-the-art image-text classification method on the full-shot datasets. Our method achieves similar improvements across few-shot regimes. Code is available at https://github.com/emu1729/GIST.

AnyStar: Domain randomized universal star-convex 3D instance segmentation

Star-convex shapes arise across bio-microscopy and radiology in the form of nuclei, nodules, metastases, and other units. Existing instance segmentation networks for such structures train on densely labeled instances for each dataset, which requires substantial and often impractical manual annotation effort. Further, significant reengineering or finetuning is needed when presented with new datasets and imaging modalities due to changes in contrast, shape, orientation, resolution, and density. We present AnyStar, a domain-randomized generative model that simulates synthetic training data of blob-like objects with randomized appearance, environments, and imaging physics to train general-purpose star-convex instance segmentation networks. As a result, networks trained using our generative model do not require annotated images from unseen datasets. A single network trained on our synthesized data accurately 3D segments C. elegans and P. dumerilii nuclei in fluorescence microscopy, mouse cortical nuclei in micro-CT, zebrafish brain nuclei in EM, and placental cotyledons in human fetal MRI, all without any retraining, finetuning, transfer learning, or domain adaptation. Code is available at https://github.com/neel-dey/AnyStar.

Empirical Analysis of a Segmentation Foundation Model in Prostate Imaging

Most state-of-the-art techniques for medical image segmentation rely on deep-learning models. These models, however, are often trained on narrowly-defined tasks in a supervised fashion, which requires expensive labeled datasets. Recent advances in several machine learning domains, such as natural language generation have demonstrated the feasibility and utility of building foundation models that can be customized for various downstream tasks with little to no labeled data. This likely represents a paradigm shift for medical imaging, where we expect that foundation models may shape the future of the field. In this paper, we consider a recently developed foundation model for medical image segmentation, UniverSeg. We conduct an empirical evaluation study in the context of prostate imaging and compare it against the conventional approach of training a task-specific segmentation model. Our results and discussion highlight several important factors that will likely be important in the development and adoption of foundation models for medical image segmentation.

Neuralizer: General Neuroimage Analysis without Re-Training

Neuroimage processing tasks like segmentation, reconstruction, and registration are central to the study of neuroscience. Robust deep learning strategies and architectures used to solve these tasks are often similar. Yet, when presented with a new task or a dataset with different visual characteristics, practitioners most often need to train a new model, or fine-tune an existing one. This is a time-consuming process that poses a substantial barrier for the thousands of neuroscientists and clinical researchers who often lack the resources or machine-learning expertise to train deep learning models. In practice, this leads to a lack of adoption of deep learning, and neuroscience tools being dominated by classical frameworks. We introduce Neuralizer, a single model that generalizes to previously unseen neuroimaging tasks and modalities without the need for re-training or fine-tuning. Tasks do not have to be known a priori, and generalization happens in a single forward pass during inference. The model can solve processing tasks across multiple image modalities, acquisition methods, and datasets, and generalize to tasks and modalities it has not been trained on. Our experiments on coronal slices show that when few annotated subjects are available, our multi-task network outperforms task-specific baselines without training on the task.

Multi-Head Graph Convolutional Network for Structural Connectome Classification

We tackle classification based on brain connectivity derived from diffusion magnetic resonance images. We propose a machine-learning model inspired by graph convolutional networks (GCNs), which takes a brain connectivity input graph and processes the data separately through a parallel GCN mechanism with multiple heads. The proposed network is a simple design that employs different heads involving graph convolutions focused on edges and nodes, capturing representations from the input data thoroughly. To test the ability of our model to extract complementary and representative features from brain connectivity data, we chose the task of sex classification. This quantifies the degree to which the connectome varies depending on the sex, which is important for improving our understanding of health and disease in both sexes. We show experiments on two publicly available datasets: PREVENT-AD (347 subjects) and OASIS3 (771 subjects). The proposed model demonstrates the highest performance compared to the existing machine-learning algorithms we tested, including classical methods and (graph and non-graph) deep learning. We provide a detailed analysis of each component of our model.

Learning Task-Specific Strategies for Accelerated MRI

Compressed sensing magnetic resonance imaging (CS-MRI) seeks to recover visual information from subsampled measurements for diagnostic tasks. Traditional CS-MRI methods often separately address measurement subsampling, image reconstruction, and task prediction, resulting in suboptimal end-to-end performance. In this work, we propose TACKLE as a unified framework for designing CS-MRI systems tailored to specific tasks. Leveraging recent co-design techniques, TACKLE jointly optimizes subsampling, reconstruction, and prediction strategies to enhance the performance on the downstream task. Our results on multiple public MRI datasets show that the proposed framework achieves improved performance on various tasks over traditional CS-MRI methods. We also evaluate the generalization ability of TACKLE by experimentally collecting a new dataset using different acquisition setups from the training data. Without additional fine-tuning, TACKLE functions robustly and leads to both numerical and visual improvements.

A robust and interpretable deep learning framework for multi-modal registration via keypoints

We present KeyMorph, a deep learning-based image registration framework that relies on automatically detecting corresponding keypoints. State-of-the-art deep learning methods for registration often are not robust to large misalignments, are not interpretable, and do not incorporate the symmetries of the problem. In addition, most models produce only a single prediction at test-time. Our core insight which addresses these shortcomings is that corresponding keypoints between images can be used to obtain the optimal transformation via a differentiable closed-form expression. We use this observation to drive the end-to-end learning of keypoints tailored for the registration task, and without knowledge of ground-truth keypoints. This framework not only leads to substantially more robust registration but also yields better interpretability, since the keypoints reveal which parts of the image are driving the final alignment. Moreover, KeyMorph can be designed to be equivariant under image translations and/or symmetric with respect to the input image ordering. Finally, we show how multiple deformation fields can be computed efficiently and in closed-form at test time corresponding to different transformation variants. We demonstrate the proposed framework in solving 3D affine and spline-based registration of multi-modal brain MRI scans. In particular, we show registration accuracy that surpasses current state-of-the-art methods, especially in the context of large displacements. Our code is available at https://github.com/evanmy/keymorph.