Researcher profile

Marc Niethammer

Marc Niethammer contributes to research discovery and scholarly infrastructure.

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Computer Vision eess.IV Machine Learning Quantitative Methods Applications physics.med-ph

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preprint2026arXiv

Stop Holding Your Breath: CT-Informed Gaussian Splatting for Dynamic Bronchoscopy

Bronchoscopic navigation relies on registering endoscopic video to a preoperative CT scan, but respiratory motion deforms the airway by 5-20 mm, creating CT-to-body divergence that limits localization accuracy. In practice, this is mitigated through breath-hold protocols, which attempt to match the intraoperative anatomy to a static CT, but are difficult to reproduce and disrupt clinical workflow. We propose to eliminate the need for breath-hold protocols by leveraging patient-specific respiratory modeling. Paired inhale-exhale CT scans, already acquired for planning, implicitly define the patient-specific deformation space of the breathing airway. By registering these scans, we reduce respiratory motion to a single scalar breathing phase per frame, constraining all reconstructions to anatomically observed configurations. We embed this representation within a mesh-anchored Gaussian splatting framework, where a lightweight estimator infers breathing phase directly from endoscopic RGB, enabling continuous, deformation-aware reconstruction throughout the respiratory cycle without breath-holds or external sensing. To enable quantitative evaluation, we introduce RESPIRE, a physically grounded bronchoscopy simulation pipeline with per-frame ground truth for geometry, pose, breathing phase, and deformation. Experiments on RESPIRE show that our approach achieves geometrically faithful reconstruction, over 20x faster training, and 1.22 mm target localization accuracy (within the 3mm clinically relevant tolerances) outperforming unconstrained single-CT baselines. Please check out our website for additional visuals: https://asdunnbe.github.io/RESPIRE/

preprint2026arXiv

TeDiO: Temporal Diagonal Optimization for Training-Free Coherent Video Diffusion

Recent text-to-video diffusion transformers generate visually compelling frames, yet still struggle with temporal coherence, often producing flickering, drifting, or unstable motion. We show that these failures leave a clear imprint inside the model: incoherent videos consistently exhibit irregular, fragmented temporal diagonals in their intermediate self-attention maps, whereas stable motion corresponds to smooth, band-diagonal patterns. Building on this observation, we introduce TeDiO, a training-free, inference-time method that reinforces temporal consistency by regularizing these internal attention patterns. TeDiO estimates diagonal smoothness, identifies unstable regions, and performs lightweight latent updates that promote coherent frame-to-frame dynamics, without modifying model weights or using external motion supervision. Across multiple video diffusion models (e.g., Wan2.1, CogVideoX), TeDiO delivers markedly smoother motion while preserving per-frame visual quality, offering an efficient plug-and-play approach to improving dynamic realism in modern video generation systems.

preprint2023arXiv

On Measuring Excess Capacity in Neural Networks

We study the excess capacity of deep networks in the context of supervised classification. That is, given a capacity measure of the underlying hypothesis class - in our case, empirical Rademacher complexity - to what extent can we (a priori) constrain this class while retaining an empirical error on a par with the unconstrained regime? To assess excess capacity in modern architectures (such as residual networks), we extend and unify prior Rademacher complexity bounds to accommodate function composition and addition, as well as the structure of convolutions. The capacity-driving terms in our bounds are the Lipschitz constants of the layers and an (2, 1) group norm distance to the initializations of the convolution weights. Experiments on benchmark datasets of varying task difficulty indicate that (1) there is a substantial amount of excess capacity per task, and (2) capacity can be kept at a surprisingly similar level across tasks. Overall, this suggests a notion of compressibility with respect to weight norms, complementary to classic compression via weight pruning. Source code is available at https://github.com/rkwitt/excess_capacity.

preprint2022arXiv

Aladdin: Joint Atlas Building and Diffeomorphic Registration Learning with Pairwise Alignment

Atlas building and image registration are important tasks for medical image analysis. Once one or multiple atlases from an image population have been constructed, commonly (1) images are warped into an atlas space to study intra-subject or inter-subject variations or (2) a possibly probabilistic atlas is warped into image space to assign anatomical labels. Atlas estimation and nonparametric transformations are computationally expensive as they usually require numerical optimization. Additionally, previous approaches for atlas building often define similarity measures between a fuzzy atlas and each individual image, which may cause alignment difficulties because a fuzzy atlas does not exhibit clear anatomical structures in contrast to the individual images. This work explores using a convolutional neural network (CNN) to jointly predict the atlas and a stationary velocity field (SVF) parameterization for diffeomorphic image registration with respect to the atlas. Our approach does not require affine pre-registrations and utilizes pairwise image alignment losses to increase registration accuracy. We evaluate our model on 3D knee magnetic resonance images (MRI) from the OAI-ZIB dataset. Our results show that the proposed framework achieves better performance than other state-of-the-art image registration algorithms, allows for end-to-end training, and for fast inference at test time.

preprint2022arXiv

Deep Decomposition for Stochastic Normal-Abnormal Transport

Advection-diffusion equations describe a large family of natural transport processes, e.g., fluid flow, heat transfer, and wind transport. They are also used for optical flow and perfusion imaging computations. We develop a machine learning model, D^2-SONATA, built upon a stochastic advection-diffusion equation, which predicts the velocity and diffusion fields that drive 2D/3D image time-series of transport. In particular, our proposed model incorporates a model of transport atypicality, which isolates abnormal differences between expected normal transport behavior and the observed transport. In a medical context such a normal-abnormal decomposition can be used, for example, to quantify pathologies. Specifically, our model identifies the advection and diffusion contributions from the transport time-series and simultaneously predicts an anomaly value field to provide a decomposition into normal and abnormal advection and diffusion behavior. To achieve improved estimation performance for the velocity and diffusion-tensor fields underlying the advection-diffusion process and for the estimation of the anomaly fields, we create a 2D/3D anomaly-encoded advection-diffusion simulator, which allows for supervised learning. We further apply our model on a brain perfusion dataset from ischemic stroke patients via transfer learning. Extensive comparisons demonstrate that our model successfully distinguishes stroke lesions (abnormal) from normal brain regions, while reconstructing the underlying velocity and diffusion tensor fields.

preprint2022arXiv

Fluid registration between lung CT and stationary chest tomosynthesis images

Registration is widely used in image-guided therapy and image-guided surgery to estimate spatial correspondences between organs of interest between planning and treatment images. However, while high-quality computed tomography (CT) images are often available at planning time, limited angle acquisitions are frequently used during treatment because of radiation concerns or imaging time constraints. This requires algorithms to register CT images based on limited angle acquisitions. We, therefore, formulate a 3D/2D registration approach which infers a 3D deformation based on measured projections and digitally reconstructed radiographs of the CT. Most 3D/2D registration approaches use simple transformation models or require complex mathematical derivations to formulate the underlying optimization problem. Instead, our approach entirely relies on differentiable operations which can be combined with modern computational toolboxes supporting automatic differentiation. This then allows for rapid prototyping, integration with deep neural networks, and to support a variety of transformation models including fluid flow models. We demonstrate our approach for the registration between CT and stationary chest tomosynthesis (sDCT) images and show how it naturally leads to an iterative image reconstruction approach.

preprint2022arXiv

iSegFormer: Interactive Segmentation via Transformers with Application to 3D Knee MR Images

We propose iSegFormer, a memory-efficient transformer that combines a Swin transformer with a lightweight multilayer perceptron (MLP) decoder. With the efficient Swin transformer blocks for hierarchical self-attention and the simple MLP decoder for aggregating both local and global attention, iSegFormer learns powerful representations while achieving high computational efficiencies. Specifically, we apply iSegFormer to interactive 3D medical image segmentation.

preprint2022arXiv

Optimal Transport Features for Morphometric Population Analysis

Brain pathologies often manifest as partial or complete loss of tissue. The goal of many neuroimaging studies is to capture the location and amount of tissue changes with respect to a clinical variable of interest, such as disease progression. Morphometric analysis approaches capture local differences in the distribution of tissue or other quantities of interest in relation to a clinical variable. We propose to augment morphometric analysis with an additional feature extraction step based on unbalanced optimal transport. The optimal transport feature extraction step increases statistical power for pathologies that cause spatially dispersed tissue loss, minimizes sensitivity to shifts due to spatial misalignment or differences in brain topology, and separates changes due to volume differences from changes due to tissue location. We demonstrate the proposed optimal transport feature extraction step in the context of a volumetric morphometric analysis of the OASIS-1 study for Alzheimer's disease. The results demonstrate that the proposed approach can identify tissue changes and differences that are not otherwise measurable.

preprint2022arXiv

PseudoClick: Interactive Image Segmentation with Click Imitation

The goal of click-based interactive image segmentation is to obtain precise object segmentation masks with limited user interaction, i.e., by a minimal number of user clicks. Existing methods require users to provide all the clicks: by first inspecting the segmentation mask and then providing points on mislabeled regions, iteratively. We ask the question: can our model directly predict where to click, so as to further reduce the user interaction cost? To this end, we propose {\PseudoClick}, a generic framework that enables existing segmentation networks to propose candidate next clicks. These automatically generated clicks, termed pseudo clicks in this work, serve as an imitation of human clicks to refine the segmentation mask.

preprint2020arXiv

A Deep Network for Joint Registration and Reconstruction of Images with Pathologies

Registration of images with pathologies is challenging due to tissue appearance changes and missing correspondences caused by the pathologies. Moreover, mass effects as observed for brain tumors may displace tissue, creating larger deformations over time than what is observed in a healthy brain. Deep learning models have successfully been applied to image registration to offer dramatic speed up and to use surrogate information (e.g., segmentations) during training. However, existing approaches focus on learning registration models using images from healthy patients. They are therefore not designed for the registration of images with strong pathologies for example in the context of brain tumors, and traumatic brain injuries. In this work, we explore a deep learning approach to register images with brain tumors to an atlas. Our model learns an appearance mapping from images with tumors to the atlas, while simultaneously predicting the transformation to atlas space. Using separate decoders, the network disentangles the tumor mass effect from the reconstruction of quasi-normal images. Results on both synthetic and real brain tumor scans show that our approach outperforms cost function masking for registration to the atlas and that reconstructed quasi-normal images can be used for better longitudinal registrations.

preprint2020arXiv

Anatomical Data Augmentation via Fluid-based Image Registration

We introduce a fluid-based image augmentation method for medical image analysis. In contrast to existing methods, our framework generates anatomically meaningful images via interpolation from the geodesic subspace underlying given samples. Our approach consists of three steps: 1) given a source image and a set of target images, we construct a geodesic subspace using the Large Deformation Diffeomorphic Metric Mapping (LDDMM) model; 2) we sample transformations from the resulting geodesic subspace; 3) we obtain deformed images and segmentations via interpolation. Experiments on brain (LPBA) and knee (OAI) data illustrate the performance of our approach on two tasks: 1) data augmentation during training and testing for image segmentation; 2) one-shot learning for single atlas image segmentation. We demonstrate that our approach generates anatomically meaningful data and improves performance on these tasks over competing approaches. Code is available at https://github.com/uncbiag/easyreg.

preprint2020arXiv

Deep Goal-Oriented Clustering

Clustering and prediction are two primary tasks in the fields of unsupervised and supervised learning, respectively. Although much of the recent advances in machine learning have been centered around those two tasks, the interdependent, mutually beneficial relationship between them is rarely explored. One could reasonably expect appropriately clustering the data would aid the downstream prediction task and, conversely, a better prediction performance for the downstream task could potentially inform a more appropriate clustering strategy. In this work, we focus on the latter part of this mutually beneficial relationship. To this end, we introduce Deep Goal-Oriented Clustering (DGC), a probabilistic framework that clusters the data by jointly using supervision via side-information and unsupervised modeling of the inherent data structure in an end-to-end fashion. We show the effectiveness of our model on a range of datasets by achieving prediction accuracies comparable to the state-of-the-art, while, more importantly in our setting, simultaneously learning congruent clustering strategies.

preprint2020arXiv

Joint and individual analysis of breast cancer histologic images and genomic covariates

A key challenge in modern data analysis is understanding connections between complex and differing modalities of data. For example, two of the main approaches to the study of breast cancer are histopathology (analyzing visual characteristics of tumors) and genetics. While histopathology is the gold standard for diagnostics and there have been many recent breakthroughs in genetics, there is little overlap between these two fields. We aim to bridge this gap by developing methods based on Angle-based Joint and Individual Variation Explained (AJIVE) to directly explore similarities and differences between these two modalities. Our approach exploits Convolutional Neural Networks (CNNs) as a powerful, automatic method for image feature extraction to address some of the challenges presented by statistical analysis of histopathology image data. CNNs raise issues of interpretability that we address by developing novel methods to explore visual modes of variation captured by statistical algorithms (e.g. PCA or AJIVE) applied to CNN features. Our results provide many interpretable connections and contrasts between histopathology and genetics.

preprint2020arXiv

Perfusion Imaging: A Data Assimilation Approach

Perfusion imaging (PI) is clinically used to assess strokes and brain tumors. Commonly used PI approaches based on magnetic resonance imaging (MRI) or computed tomography (CT) measure the effect of a contrast agent moving through blood vessels and into tissue. Contrast-agent free approaches, for example, based on intravoxel incoherent motion, also exist, but are so far not routinely used clinically. These methods rely on estimating on the arterial input function (AIF) to approximately model tissue perfusion, neglecting spatial dependencies, and reliably estimating the AIF is also non-trivial, leading to difficulties with standardizing perfusion measures. In this work we therefore propose a data-assimilation approach (PIANO) which estimates the velocity and diffusion fields of an advection-diffusion model that best explains the contrast dynamics. PIANO accounts for spatial dependencies and neither requires estimating the AIF nor relies on a particular contrast agent bolus shape. Specifically, we propose a convenient parameterization of the estimation problem, a numerical estimation approach, and extensively evaluate PIANO. We demonstrate that PIANO can successfully resolve velocity and diffusion field ambiguities and results in sensitive measures for the assessment of stroke, comparing favorably to conventional measures of perfusion.

preprint2020arXiv

VoteNet+ : An Improved Deep Learning Label Fusion Method for Multi-atlas Segmentation

In this work, we improve the performance of multi-atlas segmentation (MAS) by integrating the recently proposed VoteNet model with the joint label fusion (JLF) approach. Specifically, we first illustrate that using a deep convolutional neural network to predict atlas probabilities can better distinguish correct atlas labels from incorrect ones than relying on image intensity difference as is typical in JLF. Motivated by this finding, we propose VoteNet+, an improved deep network to locally predict the probability of an atlas label to differs from the label of the target image. Furthermore, we show that JLF is more suitable for the VoteNet framework as a label fusion method than plurality voting. Lastly, we use Platt scaling to calibrate the probabilities of our new model. Results on LPBA40 3D MR brain images show that our proposed method can achieve better performance than VoteNet.

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