Nicholas (Nick) Konz

Image segmentation foundation models (SFMs) like Segment Anything Model (SAM) have achieved impressive zero-shot and interactive segmentation across diverse domains. However, they struggle to segment objects with certain structures, particularly those with dense, tree-like morphology and low textural contrast from their surroundings. These failure modes are crucial for understanding the limitations of SFMs in real-world applications. To systematically study this issue, we introduce interpretable metrics quantifying object tree-likeness and textural separability. On carefully controlled synthetic experiments and real-world datasets, we show that SFM performance (e.g., SAM, SAM 2, HQ-SAM) noticeably correlates with these factors. We link these failures to "textural confusion", where models misinterpret local structure as global texture, causing over-segmentation or difficulty distinguishing objects from similar backgrounds. Notably, targeted fine-tuning fails to resolve this issue, indicating a fundamental limitation. Our study provides the first quantitative framework for modeling the behavior of SFMs on challenging structures, offering interpretable insights into their segmentation capabilities.

Foundation models, pre-trained on large image datasets and capable of capturing rich feature representations, have recently shown potential for zero-shot image registration. However, their performance has mostly been tested in the context of rigid or less complex structures, such as the brain or abdominal organs, and it remains unclear whether these models can handle more challenging, deformable anatomy. Breast MRI registration is particularly difficult due to significant anatomical variation between patients, deformation caused by patient positioning, and the presence of thin and complex internal structure of fibroglandular tissue, where accurate alignment is crucial. Whether foundation model-based registration algorithms can address this level of complexity remains an open question. In this study, we provide a comprehensive evaluation of foundation model-based registration algorithms for breast MRI. We assess five pre-trained encoders, including DINO-v2, SAM, MedSAM, SSLSAM, and MedCLIP, across four key breast registration tasks that capture variations in different years and dates, sequences, modalities, and patient disease status (lesion versus no lesion). Our results show that foundation model-based algorithms such as SAM outperform traditional registration baselines for overall breast alignment, especially under large domain shifts, but struggle with capturing fine details of fibroglandular tissue. Interestingly, additional pre-training or fine-tuning on medical or breast-specific images in MedSAM and SSLSAM, does not improve registration performance and may even decrease it in some cases. Further work is needed to understand how domain-specific training influences registration and to explore targeted strategies that improve both global alignment and fine structure accuracy. We also publicly release our code at https://github.com/mazurowski-lab/Foundation-based-reg.

Determining whether two sets of images belong to the same or different distributions or domains is a crucial task in modern medical image analysis and deep learning; for example, to evaluate the output quality of image generative models. Currently, metrics used for this task either rely on the (potentially biased) choice of some downstream task, such as segmentation, or adopt task-independent perceptual metrics (\eg, Fréchet Inception Distance/FID) from natural imaging, which we show insufficiently capture anatomical features. To this end, we introduce a new perceptual metric tailored for medical images, FRD (Fréchet Radiomic Distance), which utilizes standardized, clinically meaningful, and interpretable image features. We show that FRD is superior to other image distribution metrics for a range of medical imaging applications, including out-of-domain (OOD) detection, the evaluation of image-to-image translation (by correlating more with downstream task performance as well as anatomical consistency and realism), and the evaluation of unconditional image generation. Moreover, FRD offers additional benefits such as stability and computational efficiency at low sample sizes, sensitivity to image corruptions and adversarial attacks, feature interpretability, and correlation with radiologist-perceived image quality. Additionally, we address key gaps in the literature by presenting an extensive framework for the multifaceted evaluation of image similarity metrics in medical imaging—including the first large-scale comparative study of generative models for medical image translation—and release an accessible codebase to facilitate future research. Our results are supported by thorough experiments spanning a variety of datasets, modalities, and downstream tasks, highlighting the broad potential of FRD for medical image analysis.

This paper investigates discrepancies in how neural networks learn from different imaging domains, which are commonly overlooked when adopting computer vision techniques from the domain of natural images to other specialized domains such as medical images. Recent works have found that the generalization error of a trained network typically increases with the intrinsic dimension (d_data) of its training set. Yet, the steepness of this relationship varies significantly between medical (radiological) and natural imaging domains, with no existing theoretical explanation. We address this gap in knowledge by establishing and empirically validating a generalization scaling law with respect to d_data, and propose that the substantial scaling discrepancy between the two considered domains may be at least partially attributed to the higher intrinsic “label sharpness” (K_F) of medical imaging datasets, a metric which we propose. Next, we demonstrate an additional benefit of measuring the label sharpness of a training set: it is negatively correlated with the trained model’s adversarial robustness, which notably leads to models for medical images having a substantially higher vulnerability to adversarial attack. Finally, we extend our d_data formalism to the related metric of learned representation intrinsic dimension (d_repr), derive a generalization scaling law with respect to d_repr, and show that d_data serves as an upper bound for d_repr. Our theoretical results are supported by thorough experiments with six models and eleven natural and medical imaging datasets over a range of training set sizes. Our findings offer insights into the influence of intrinsic dataset properties on generalization, representation learning, and robustness in deep neural networks. Code link: https://github.com/mazurowski-lab/intrinsic-properties.

Diffusion models have enabled remarkably high-quality medical image generation, yet it is challenging to enforce anatomical constraints in generated images. To this end, we propose a diffusion model-based method that supports anatomically-controllable medical image generation, by following a multi-class anatomical segmentation mask at each sampling step. We additionally introduce a random mask ablation training algorithm to enable conditioning on a selected combination of anatomical constraints while allowing flexibility in other anatomical areas. We compare our method ("SegGuidedDiff") to existing methods on breast MRI and abdominal/neck-to-pelvis CT datasets with a wide range of anatomical objects. Results show that our method reaches a new state-of-the-art in the faithfulness of generated images to input anatomical masks on both datasets, and is on par for general anatomical realism. Finally, our model also enjoys the extra benefit of being able to adjust the anatomical similarity of generated images to real images of choice through interpolation in its latent space. SegGuidedDiff has many applications, including cross-modality translation, and the generation of paired or counterfactual data. Our code is available at https://github.com/mazurowski-lab/segmentation-guided-diffusion.