Neel Dey

Nalini M. Singh, Neel Dey, Malte Hoffmann et al. · mit

Motion artifacts are a pervasive problem in MRI, leading to misdiagnosis or mischaracterization in population-level imaging studies. Current retrospective rigid intra-slice motion correction techniques jointly optimize estimates of the image and the motion parameters. In this paper, we use a deep network to reduce the joint image-motion parameter search to a search over rigid motion parameters alone. Our network produces a reconstruction as a function of two inputs: corrupted k-space data and motion parameters. We train the network using simulated, motion-corrupted k-space data generated with known motion parameters. At test-time, we estimate unknown motion parameters by minimizing a data consistency loss between the motion parameters, the network-based image reconstruction given those parameters, and the acquired measurements. Intra-slice motion correction experiments on simulated and realistic 2D fast spin echo brain MRI achieve high reconstruction fidelity while providing the benefits of explicit data consistency optimization. Our code is publicly available at https://www.github.com/nalinimsingh/neuroMoCo.

Neel Dey, S. Mazdak Abulnaga, Benjamin Billot et al. · mit

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.

Axel Elaldi, Guido Gerig, Neel Dey · mit

We present Roto-Translation Equivariant Spherical Deconvolution (RT-ESD), an $E(3)\times SO(3)$ equivariant framework for sparse deconvolution of volumes where each voxel contains a spherical signal. Such 6D data naturally arises in diffusion MRI (dMRI), a medical imaging modality widely used to measure microstructure and structural connectivity. As each dMRI voxel is typically a mixture of various overlapping structures, there is a need for blind deconvolution to recover crossing anatomical structures such as white matter tracts. Existing dMRI work takes either an iterative or deep learning approach to sparse spherical deconvolution, yet it typically does not account for relationships between neighboring measurements. This work constructs equivariant deep learning layers which respect to symmetries of spatial rotations, reflections, and translations, alongside the symmetries of voxelwise spherical rotations. As a result, RT-ESD improves on previous work across several tasks including fiber recovery on the DiSCo dataset, deconvolution-derived partial volume estimation on real-world \textit{in vivo} human brain dMRI, and improved downstream reconstruction of fiber tractograms on the Tractometer dataset. Our implementation is available at https://github.com/AxelElaldi/e3so3_conv

Zeen Chi, Zhongxiao Cong, Clinton J. Wang et al. · mit

We present a method for fast biomedical image atlas construction using neural fields. Atlases are key to biomedical image analysis tasks, yet conventional and deep network estimation methods remain time-intensive. In this preliminary work, we frame subject-specific atlas building as learning a neural field of deformable spatiotemporal observations. We apply our method to learning subject-specific atlases and motion stabilization of dynamic BOLD MRI time-series of fetuses in utero. Our method yields high-quality atlases of fetal BOLD time-series with $\sim$5-7$\times$ faster convergence compared to existing work. While our method slightly underperforms well-tuned baselines in terms of anatomical overlap, it estimates templates significantly faster, thus enabling rapid processing and stabilization of large databases of 4D dynamic MRI acquisitions. Code is available at https://github.com/Kidrauh/neural-atlasing

Sebo Diaz, Polina Golland, Elfar Adalsteinsson et al. · mit

We present DropGen, a simple and theoretically-grounded approach for domain generalization in 3D biomedical image segmentation. Modern segmentation models degrade sharply under shifts in modality, disease severity, clinical sites, and other factors, creating brittle models that limit reliable deployment. Existing domain generalization methods rely on extreme augmentations, mixing domain statistics, or architectural redesigns, yet incur significant implementation overhead and yield inconsistent performance across biomedical settings. DropGen instead proposes a principled learning strategy with minimal overhead that leverages both source-domain image intensities and domain-stable foundation model representations to train robust segmentation models. As a result, DropGen achieves strong gains in both fully supervised and few-shot segmentation across a broad range of shifts in biomedical studies. Unlike prior approaches, DropGen is architecture- and loss-agnostic, compatible with standard augmentation pipelines, computationally lightweight, and tackles arbitrary anatomical regions. Our implementation is freely available at https://github.com/sebodiaz/DropGen.

Yingcheng Liu, Neerav Karani, Neel Dey et al. · mit

The placenta plays a crucial role in fetal development. Automated 3D placenta segmentation from fetal EPI MRI holds promise for advancing prenatal care. This paper proposes an effective semi-supervised learning method for improving placenta segmentation in fetal EPI MRI time series. We employ consistency regularization loss that promotes consistency under spatial transformation of the same image and temporal consistency across nearby images in a time series. The experimental results show that the method improves the overall segmentation accuracy and provides better performance for outliers and hard samples. The evaluation also indicates that our method improves the temporal coherency of the prediction, which could lead to more accurate computation of temporal placental biomarkers. This work contributes to the study of the placenta and prenatal clinical decision-making. Code is available at https://github.com/firstmover/cr-seg.

Mengwei Ren, Neel Dey, Martin A. Styner et al. · mit

Recent self-supervised advances in medical computer vision exploit global and local anatomical self-similarity for pretraining prior to downstream tasks such as segmentation. However, current methods assume i.i.d. image acquisition, which is invalid in clinical study designs where follow-up longitudinal scans track subject-specific temporal changes. Further, existing self-supervised methods for medically-relevant image-to-image architectures exploit only spatial or temporal self-similarity and only do so via a loss applied at a single image-scale, with naive multi-scale spatiotemporal extensions collapsing to degenerate solutions. To these ends, this paper makes two contributions: (1) It presents a local and multi-scale spatiotemporal representation learning method for image-to-image architectures trained on longitudinal images. It exploits the spatiotemporal self-similarity of learned multi-scale intra-subject features for pretraining and develops several feature-wise regularizations that avoid collapsed identity representations; (2) During finetuning, it proposes a surprisingly simple self-supervised segmentation consistency regularization to exploit intra-subject correlation. Benchmarked in the one-shot segmentation setting, the proposed framework outperforms both well-tuned randomly-initialized baselines and current self-supervised techniques designed for both i.i.d. and longitudinal datasets. These improvements are demonstrated across both longitudinal neurodegenerative adult MRI and developing infant brain MRI and yield both higher performance and longitudinal consistency.

Neel Dey, Jo Schlemper, Seyed Sadegh Mohseni Salehi et al. · mit

Establishing voxelwise semantic correspondence across distinct imaging modalities is a foundational yet formidable computer vision task. Current multi-modality registration techniques maximize hand-crafted inter-domain similarity functions, are limited in modeling nonlinear intensity-relationships and deformations, and may require significant re-engineering or underperform on new tasks, datasets, and domain pairs. This work presents ContraReg, an unsupervised contrastive representation learning approach to multi-modality deformable registration. By projecting learned multi-scale local patch features onto a jointly learned inter-domain embedding space, ContraReg obtains representations useful for non-rigid multi-modality alignment. Experimentally, ContraReg achieves accurate and robust results with smooth and invertible deformations across a series of baselines and ablations on a neonatal T1-T2 brain MRI registration task with all methods validated over a wide range of deformation regularization strengths.

Bo Zhou, Jo Schlemper, Neel Dey et al. · mit

While enabling accelerated acquisition and improved reconstruction accuracy, current deep MRI reconstruction networks are typically supervised, require fully sampled data, and are limited to Cartesian sampling patterns. These factors limit their practical adoption as fully-sampled MRI is prohibitively time-consuming to acquire clinically. Further, non-Cartesian sampling patterns are particularly desirable as they are more amenable to acceleration and show improved motion robustness. To this end, we present a fully self-supervised approach for accelerated non-Cartesian MRI reconstruction which leverages self-supervision in both k-space and image domains. In training, the undersampled data are split into disjoint k-space domain partitions. For the k-space self-supervision, we train a network to reconstruct the input undersampled data from both the disjoint partitions and from itself. For the image-level self-supervision, we enforce appearance consistency obtained from the original undersampled data and the two partitions. Experimental results on our simulated multi-coil non-Cartesian MRI dataset demonstrate that DDSS can generate high-quality reconstruction that approaches the accuracy of the fully supervised reconstruction, outperforming previous baseline methods. Finally, DDSS is shown to scale to highly challenging real-world clinical MRI reconstruction acquired on a portable low-field (0.064 T) MRI scanner with no data available for supervised training while demonstrating improved image quality as compared to traditional reconstruction, as determined by a radiologist study.

Neerav Karani, Neel Dey, Polina Golland · mit

Neural network prediction probabilities and accuracy are often only weakly-correlated. Inherent label ambiguity in training data for image segmentation aggravates such miscalibration. We show that logit consistency across stochastic transformations acts as a spatially varying regularizer that prevents overconfident predictions at pixels with ambiguous labels. Our boundary-weighted extension of this regularizer provides state-of-the-art calibration for prostate and heart MRI segmentation.

Yiming Chen, Niharika S. D'Souza, Akshith Mandepally et al. · mit

Precisely estimating lumen boundaries in intravascular ultrasound (IVUS) is needed for sizing interventional stents to treat deep vein thrombosis (DVT). Unfortunately, current segmentation networks like the UNet lack the precision needed for clinical adoption in IVUS workflows. This arises due to the difficulty of automatically learning accurate lumen contour from limited training data while accounting for the radial geometry of IVUS imaging. We propose the Geo-UNet framework to address these issues via a design informed by the geometry of the lumen contour segmentation task. We first convert the input data and segmentation targets from Cartesian to polar coordinates. Starting from a convUNet feature extractor, we propose a two-task setup, one for conventional pixel-wise labeling and the other for single boundary lumen-contour localization. We directly combine the two predictions by passing the predicted lumen contour through a new activation (named CDFeLU) to filter out spurious pixel-wise predictions. Our unified loss function carefully balances area-based, distance-based, and contour-based penalties to provide near clinical-grade generalization in unseen patient data. We also introduce a lightweight, inference-time technique to enhance segmentation smoothness. The efficacy of our framework on a venous IVUS dataset is shown against state-of-the-art models.

Vivek Gopalakrishnan, Neel Dey, Polina Golland · mit

Surgical decisions are informed by aligning rapid portable 2D intraoperative images (e.g., X-rays) to a high-fidelity 3D preoperative reference scan (e.g., CT). 2D/3D image registration often fails in practice: conventional optimization methods are prohibitively slow and susceptible to local minima, while neural networks trained on small datasets fail on new patients or require impractical landmark supervision. We present DiffPose, a self-supervised approach that leverages patient-specific simulation and differentiable physics-based rendering to achieve accurate 2D/3D registration without relying on manually labeled data. Preoperatively, a CNN is trained to regress the pose of a randomly oriented synthetic X-ray rendered from the preoperative CT. The CNN then initializes rapid intraoperative test-time optimization that uses the differentiable X-ray renderer to refine the solution. Our work further proposes several geometrically principled methods for sampling camera poses from $\mathbf{SE}(3)$, for sparse differentiable rendering, and for driving registration in the tangent space $\mathfrak{se}(3)$ with geodesic and multiscale locality-sensitive losses. DiffPose achieves sub-millimeter accuracy across surgical datasets at intraoperative speeds, improving upon existing unsupervised methods by an order of magnitude and even outperforming supervised baselines. Our code is available at https://github.com/eigenvivek/DiffPose.

Benjamin Billot, Neel Dey, Daniel Moyer et al. · mit

Rigid motion tracking is paramount in many medical imaging applications where movements need to be detected, corrected, or accounted for. Modern strategies rely on convolutional neural networks (CNN) and pose this problem as rigid registration. Yet, CNNs do not exploit natural symmetries in this task, as they are equivariant to translations (their outputs shift with their inputs) but not to rotations. Here we propose EquiTrack, the first method that uses recent steerable SE(3)-equivariant CNNs (E-CNN) for motion tracking. While steerable E-CNNs can extract corresponding features across different poses, testing them on noisy medical images reveals that they do not have enough learning capacity to learn noise invariance. Thus, we introduce a hybrid architecture that pairs a denoiser with an E-CNN to decouple the processing of anatomically irrelevant intensity features from the extraction of equivariant spatial features. Rigid transforms are then estimated in closed-form. EquiTrack outperforms state-of-the-art learning and optimisation methods for motion tracking in adult brain MRI and fetal MRI time series. Our code is available at https://github.com/BBillot/EquiTrack.

Vivek Gopalakrishnan, Neel Dey, David-Dimitris Chlorogiannis et al. · mit

The integration of artificial intelligence in image-guided interventions holds transformative potential, promising to extract 3D geometric and quantitative information from conventional 2D imaging modalities during complex procedures. Achieving this requires the rapid and precise alignment of 2D intraoperative images (e.g., X-ray) with 3D preoperative volumes (e.g., CT, MRI). However, current 2D/3D registration methods fail across the broad spectrum of procedures dependent on X-ray guidance: traditional optimization techniques require custom parameter tuning for each subject, whereas neural networks trained on small datasets do not generalize to new patients or require labor-intensive manual annotations, increasing clinical burden and precluding application to new anatomical targets. To address these challenges, we present xvr, a fully automated framework for training patient-specific neural networks for 2D/3D registration. xvr uses physics-based simulation to generate abundant high-quality training data from a patient's own preoperative volumetric imaging, thereby overcoming the inherently limited ability of supervised models to generalize to new patients and procedures. Furthermore, xvr requires only 5 minutes of training per patient, making it suitable for emergency interventions as well as planned procedures. We perform the largest evaluation of a 2D/3D registration algorithm on real X-ray data to date and find that xvr robustly generalizes across a diverse dataset comprising multiple anatomical structures, imaging modalities, and hospitals. Across surgical tasks, xvr achieves submillimeter-accurate registration at intraoperative speeds, improving upon existing methods by an order of magnitude. xvr is released as open-source software freely available at https://github.com/eigenvivek/xvr.

Mohammadhossein Momeni, Vivek Gopalakrishnan, Neel Dey et al. · mit

We present DiffVox, a self-supervised framework for Cone-Beam Computed Tomography (CBCT) reconstruction by directly optimizing a voxelgrid representation using physics-based differentiable X-ray rendering. Further, we investigate how the different implementations of the X-ray image formation model in the renderer affect the quality of 3D reconstruction and novel view synthesis. When combined with our regularized voxel-based learning framework, we find that using an exact implementation of the discrete Beer-Lambert law for X-ray attenuation in the renderer outperforms both widely used iterative CBCT reconstruction algorithms and modern neural field approaches, particularly when given only a few input views. As a result, we reconstruct high-fidelity 3D CBCT volumes from fewer X-rays, potentially reducing ionizing radiation exposure and improving diagnostic utility. Our implementation is available at https://github.com/hossein-momeni/DiffVox.

S. Mazdak Abulnaga, Neel Dey, Sean I. Young et al. · mit

Blood oxygen level dependent (BOLD) MRI time series with maternal hyperoxia can assess placental oxygenation and function. Measuring precise BOLD changes in the placenta requires accurate temporal placental segmentation and is confounded by fetal and maternal motion, contractions, and hyperoxia-induced intensity changes. Current BOLD placenta segmentation methods warp a manually annotated subject-specific template to the entire time series. However, as the placenta is a thin, elongated, and highly non-rigid organ subject to large deformations and obfuscated edges, existing work cannot accurately segment the placental shape, especially near boundaries. In this work, we propose a machine learning segmentation framework for placental BOLD MRI and apply it to segmenting each volume in a time series. We use a placental-boundary weighted loss formulation and perform a comprehensive evaluation across several popular segmentation objectives. Our model is trained and tested on a cohort of 91 subjects containing healthy fetuses, fetuses with fetal growth restriction, and mothers with high BMI. Biomedically, our model performs reliably in segmenting volumes in both normoxic and hyperoxic points in the BOLD time series. We further find that boundary-weighting increases placental segmentation performance by 8.3% and 6.0% Dice coefficient for the cross-entropy and signed distance transform objectives, respectively. Our code and trained model is available at https://github.com/mabulnaga/automatic-placenta-segmentation.

Jingru Fu, Yuqi Zheng, Neel Dey et al. · mit

Simulating prospective magnetic resonance imaging (MRI) scans from a given individual brain image is challenging, as it requires accounting for canonical changes in aging and/or disease progression while also considering the individual brain's current status and unique characteristics. While current deep generative models can produce high-resolution anatomically accurate templates for population-wide studies, their ability to predict future aging trajectories for individuals remains limited, particularly in capturing subject-specific neuroanatomical variations over time. In this study, we introduce Individualized Brain Synthesis (InBrainSyn), a framework for synthesizing high-resolution subject-specific longitudinal MRI scans that simulate neurodegeneration in both Alzheimer's disease (AD) and normal aging. InBrainSyn uses a parallel transport algorithm to adapt the population-level aging trajectories learned by a generative deep template network, enabling individualized aging synthesis. As InBrainSyn uses diffeomorphic transformations to simulate aging, the synthesized images are topologically consistent with the original anatomy by design. We evaluated InBrainSyn both quantitatively and qualitatively on AD and healthy control cohorts from the Open Access Series of Imaging Studies - version 3 dataset. Experimentally, InBrainSyn can also model neuroanatomical transitions between normal aging and AD. An evaluation of an external set supports its generalizability. Overall, with only a single baseline scan, InBrainSyn synthesizes realistic 3D spatiotemporal T1w MRI scans, producing personalized longitudinal aging trajectories. The code for InBrainSyn is available at: https://github.com/Fjr9516/InBrainSyn.

Sebastian Diaz, Benjamin Billot, Neel Dey et al. · mit

Fetal motion is a critical indicator of neurological development and intrauterine health, yet its quantification remains challenging, particularly at earlier gestational ages (GA). Current methods track fetal motion by predicting the location of annotated landmarks on 3D echo planar imaging (EPI) time-series, primarily in third-trimester fetuses. The predicted landmarks enable simplification of the fetal body for downstream analysis. While these methods perform well within their training age distribution, they consistently fail to generalize to early GAs due to significant anatomical changes in both mother and fetus across gestation, as well as the difficulty of obtaining annotated early GA EPI data. In this work, we develop a cross-population data augmentation framework that enables pose estimation models to robustly generalize to younger GA clinical cohorts using only annotated images from older GA cohorts. Specifically, we introduce a fetal-specific augmentation strategy that simulates the distinct intrauterine environment and fetal positioning of early GAs. Our experiments find that cross-population augmentation yields reduced variability and significant improvements across both older GA and challenging early GA cases. By enabling more reliable pose estimation across gestation, our work potentially facilitates early clinical detection and intervention in challenging 4D fetal imaging settings. Code is available at https://github.com/sebodiaz/cross-population-pose.

Mengwei Ren, Heejong Kim, Neel Dey et al.

Current deep learning approaches for diffusion MRI modeling circumvent the need for densely-sampled diffusion-weighted images (DWIs) by directly predicting microstructural indices from sparsely-sampled DWIs. However, they implicitly make unrealistic assumptions of static $q$-space sampling during training and reconstruction. Further, such approaches can restrict downstream usage of variably sampled DWIs for usages including the estimation of microstructural indices or tractography. We propose a generative adversarial translation framework for high-quality DWI synthesis with arbitrary $q$-space sampling given commonly acquired structural images (e.g., B0, T1, T2). Our translation network linearly modulates its internal representations conditioned on continuous $q$-space information, thus removing the need for fixed sampling schemes. Moreover, this approach enables downstream estimation of high-quality microstructural maps from arbitrarily subsampled DWIs, which may be particularly important in cases with sparsely sampled DWIs. Across several recent methodologies, the proposed approach yields improved DWI synthesis accuracy and fidelity with enhanced downstream utility as quantified by the accuracy of scalar microstructure indices estimated from the synthesized images. Code is available at https://github.com/mengweiren/q-space-conditioned-dwi-synthesis.

Neel Dey, Benjamin Billot, Hallee E. Wong et al. · mit

Current volumetric biomedical foundation models struggle to generalize as public 3D datasets are small and do not cover the broad diversity of medical procedures, conditions, anatomical regions, and imaging protocols. We address this by creating a representation learning method that instead anticipates strong domain shifts at training time itself. We first propose a data engine that synthesizes highly variable training samples that would enable generalization to new biomedical contexts. To then train a single 3D network for any voxel-level task, we develop a contrastive learning method that pretrains the network to be stable against nuisance imaging variation simulated by the data engine, a key inductive bias for generalization. This network's features can be used as robust representations of input images for downstream tasks and its weights provide a strong, dataset-agnostic initialization for finetuning on new datasets. As a result, we set new standards across both multimodality registration and few-shot segmentation, a first for any 3D biomedical vision model, all without (pre-)training on any existing dataset of real images.

S. Mazdak Abulnaga, Andrew Hoopes, Neel Dey et al. · mit

We present MultiMorph, a fast and efficient method for constructing anatomical atlases on the fly. Atlases capture the canonical structure of a collection of images and are essential for quantifying anatomical variability across populations. However, current atlas construction methods often require days to weeks of computation, thereby discouraging rapid experimentation. As a result, many scientific studies rely on suboptimal, precomputed atlases from mismatched populations, negatively impacting downstream analyses. MultiMorph addresses these challenges with a feedforward model that rapidly produces high-quality, population-specific atlases in a single forward pass for any 3D brain dataset, without any fine-tuning or optimization. MultiMorph is based on a linear group-interaction layer that aggregates and shares features within the group of input images. Further, by leveraging auxiliary synthetic data, MultiMorph generalizes to new imaging modalities and population groups at test-time. Experimentally, MultiMorph outperforms state-of-the-art optimization-based and learning-based atlas construction methods in both small and large population settings, with a 100-fold reduction in time. This makes MultiMorph an accessible framework for biomedical researchers without machine learning expertise, enabling rapid, high-quality atlas generation for diverse studies.

Axel Elaldi, Guido Gerig, Neel Dey · mit

Each voxel in a diffusion MRI (dMRI) image contains a spherical signal corresponding to the direction and strength of water diffusion in the brain. This paper advances the analysis of such spatio-spherical data by developing convolutional network layers that are equivariant to the $\mathbf{E(3) \times SO(3)}$ group and account for the physical symmetries of dMRI including rotations, translations, and reflections of space alongside voxel-wise rotations. Further, neuronal fibers are typically antipodally symmetric, a fact we leverage to construct highly efficient spatio-hemispherical graph convolutions to accelerate the analysis of high-dimensional dMRI data. In the context of sparse spherical fiber deconvolution to recover white matter microstructure, our proposed equivariant network layers yield substantial performance and efficiency gains, leading to better and more practical resolution of crossing neuronal fibers and fiber tractography. These gains are experimentally consistent across both simulation and in vivo human datasets.

Vivek Gopalakrishnan, Neel Dey, Polina Golland · mit

Determining the 3D pose of a patient from a limited set of 2D X-ray images is a critical task in interventional settings. While preoperative volumetric imaging (e.g., CT and MRI) provides precise 3D localization and visualization of anatomical targets, these modalities cannot be acquired during procedures, where fast 2D imaging (X-ray) is used instead. To integrate volumetric guidance into intraoperative procedures, we present PolyPose, a simple and robust method for deformable 2D/3D registration. PolyPose parameterizes complex 3D deformation fields as a composition of rigid transforms, leveraging the biological constraint that individual bones do not bend in typical motion. Unlike existing methods that either assume no inter-joint movement or fail outright in this under-determined setting, our polyrigid formulation enforces anatomically plausible priors that respect the piecewise-rigid nature of human movement. This approach eliminates the need for expensive deformation regularizers that require patient- and procedure-specific hyperparameter optimization. Across extensive experiments on diverse datasets from orthopedic surgery and radiotherapy, we show that this strong inductive bias enables PolyPose to successfully align the patient's preoperative volume to as few as two X-rays, thereby providing crucial 3D guidance in challenging sparse-view and limited-angle settings where current registration methods fail. Additional visualizations, tutorials, and code are available at https://polypose.csail.mit.edu.

Bo Zhou, Neel Dey, Jo Schlemper et al.

Multi-contrast MRI (MC-MRI) captures multiple complementary imaging modalities to aid in radiological decision-making. Given the need for lowering the time cost of multiple acquisitions, current deep accelerated MRI reconstruction networks focus on exploiting the redundancy between multiple contrasts. However, existing works are largely supervised with paired data and/or prohibitively expensive fully-sampled MRI sequences. Further, reconstruction networks typically rely on convolutional architectures which are limited in their capacity to model long-range interactions and may lead to suboptimal recovery of fine anatomical detail. To these ends, we present a dual-domain self-supervised transformer (DSFormer) for accelerated MC-MRI reconstruction. DSFormer develops a deep conditional cascade transformer (DCCT) consisting of several cascaded Swin transformer reconstruction networks (SwinRN) trained under two deep conditioning strategies to enable MC-MRI information sharing. We further present a dual-domain (image and k-space) self-supervised learning strategy for DCCT to alleviate the costs of acquiring fully sampled training data. DSFormer generates high-fidelity reconstructions which experimentally outperform current fully-supervised baselines. Moreover, we find that DSFormer achieves nearly the same performance when trained either with full supervision or with our proposed dual-domain self-supervision.

Neel Dey, Mengwei Ren, Adrian V. Dalca et al.

Deformable templates are essential to large-scale medical image registration, segmentation, and population analysis. Current conventional and deep network-based methods for template construction use only regularized registration objectives and often yield templates with blurry and/or anatomically implausible appearance, confounding downstream biomedical interpretation. We reformulate deformable registration and conditional template estimation as an adversarial game wherein we encourage realism in the moved templates with a generative adversarial registration framework conditioned on flexible image covariates. The resulting templates exhibit significant gain in specificity to attributes such as age and disease, better fit underlying group-wise spatiotemporal trends, and achieve improved sharpness and centrality. These improvements enable more accurate population modeling with diverse covariates for standardized downstream analyses and easier anatomical delineation for structures of interest.

Shijie Li, Neel Dey, Katharina Bermond et al.

Annotation is a major hurdle in the semantic segmentation of microscopy images and volumes due to its prerequisite expertise and effort. This work enables the training of semantic segmentation networks on images with only a single point for training per instance, an extreme case of weak supervision which drastically reduces the burden of annotation. Our approach has two key aspects: (1) we construct a graph-theoretic soft-segmentation using individual seeds to be used within a regularizer during training and (2) we use an objective function that enables learning from the constructed soft-labels. We achieve competitive results against the state-of-the-art in point-supervised semantic segmentation on challenging datasets in digital pathology. Finally, we scale our methodology to point-supervised segmentation in 3D fluorescence microscopy volumes, obviating the need for arduous manual volumetric delineation. Our code is freely available.

Axel Elaldi, Neel Dey, Heejong Kim et al.

We present a rotation-equivariant unsupervised learning framework for the sparse deconvolution of non-negative scalar fields defined on the unit sphere. Spherical signals with multiple peaks naturally arise in Diffusion MRI (dMRI), where each voxel consists of one or more signal sources corresponding to anisotropic tissue structure such as white matter. Due to spatial and spectral partial voluming, clinically-feasible dMRI struggles to resolve crossing-fiber white matter configurations, leading to extensive development in spherical deconvolution methodology to recover underlying fiber directions. However, these methods are typically linear and struggle with small crossing-angles and partial volume fraction estimation. In this work, we improve on current methodologies by nonlinearly estimating fiber structures via unsupervised spherical convolutional networks with guaranteed equivariance to spherical rotation. Experimentally, we first validate our proposition via extensive single and multi-shell synthetic benchmarks demonstrating competitive performance against common baselines. We then show improved downstream performance on fiber tractography measures on the Tractometer benchmark dataset. Finally, we show downstream improvements in terms of tractography and partial volume estimation on a multi-shell dataset of human subjects.

Mengwei Ren, Neel Dey, James Fishbaugh et al.

Deep networks are now ubiquitous in large-scale multi-center imaging studies. However, the direct aggregation of images across sites is contraindicated for downstream statistical and deep learning-based image analysis due to inconsistent contrast, resolution, and noise. To this end, in the absence of paired data, variations of Cycle-consistent Generative Adversarial Networks have been used to harmonize image sets between a source and target domain. Importantly, these methods are prone to instability, contrast inversion, intractable manipulation of pathology, and steganographic mappings which limit their reliable adoption in real-world medical imaging. In this work, based on an underlying assumption that morphological shape is consistent across imaging sites, we propose a segmentation-renormalized image translation framework to reduce inter-scanner heterogeneity while preserving anatomical layout. We replace the affine transformations used in the normalization layers within generative networks with trainable scale and shift parameters conditioned on jointly learned anatomical segmentation embeddings to modulate features at every level of translation. We evaluate our methodologies against recent baselines across several imaging modalities (T1w MRI, FLAIR MRI, and OCT) on datasets with and without lesions. Segmentation-renormalization for translation GANs yields superior image harmonization as quantified by Inception distances, demonstrates improved downstream utility via post-hoc segmentation accuracy, and improved robustness to translation perturbation and self-adversarial attacks.

Guillaume Gisbert, Neel Dey, Hiroshi Ishikawa et al.

Optical Coherence Tomography (OCT) is pervasive in both the research and clinical practice of Ophthalmology. However, OCT images are strongly corrupted by noise, limiting their interpretation. Current OCT denoisers leverage assumptions on noise distributions or generate targets for training deep supervised denoisers via averaging of repeat acquisitions. However, recent self-supervised advances allow the training of deep denoising networks using only repeat acquisitions without clean targets as ground truth, reducing the burden of supervised learning. Despite the clear advantages of self-supervised methods, their use is precluded as OCT shows strong structural deformations even between sequential scans of the same subject due to involuntary eye motion. Further, direct nonlinear alignment of repeats induces correlation of the noise between images. In this paper, we propose a joint diffeomorphic template estimation and denoising framework which enables the use of self-supervised denoising for motion deformed repeat acquisitions, without empirically registering their noise realizations. Strong qualitative and quantitative improvements are achieved in denoising OCT images, with generic utility in any imaging modality amenable to multiple exposures.

Neel Dey, Antong Chen, Soheil Ghafurian

Recent improvements in generative adversarial visual synthesis incorporate real and fake image transformation in a self-supervised setting, leading to increased stability and perceptual fidelity. However, these approaches typically involve image augmentations via additional regularizers in the GAN objective and thus spend valuable network capacity towards approximating transformation equivariance instead of their desired task. In this work, we explicitly incorporate inductive symmetry priors into the network architectures via group-equivariant convolutional networks. Group-convolutions have higher expressive power with fewer samples and lead to better gradient feedback between generator and discriminator. We show that group-equivariance integrates seamlessly with recent techniques for GAN training across regularizers, architectures, and loss functions. We demonstrate the utility of our methods for conditional synthesis by improving generation in the limited data regime across symmetric imaging datasets and even find benefits for natural images with preferred orientation.