Andreas Mang

Naveen Himthani, Malte Brunn, Jae-Youn Kim et al.

We study the performance of CLAIRE -- a diffeomorphic multi-node, multi-GPU image-registration algorithm, and software -- in large-scale biomedical imaging applications with billions of voxels. At such resolutions, most existing software packages for diffeomorphic image registration are prohibitively expensive. As a result, practitioners first significantly downsample the original images and then register them using existing tools. Our main contribution is an extensive analysis of the impact of downsampling on registration performance. We study this impact by comparing full-resolution registrations obtained with CLAIRE to lower-resolution registrations for synthetic and real-world imaging datasets. Our results suggest that registration at full resolution can yield a superior registration quality -- but not always. For example, downsampling a synthetic image from $1024^3$ to $256^3$ decreases the Dice coefficient from 92% to 79%. However, the differences are less pronounced for noisy or low-contrast high-resolution images. CLAIRE allows us not only to register images of clinically relevant size in a few seconds but also to register images at unprecedented resolution in a reasonable time. The highest resolution considered is CLARITY images of size $2816\times3016\times1162$. To the best of our knowledge, this is the first study on image registration quality at such resolutions.

Hossein Dabirian, Radmir Sultamuratov, James Herring et al.

Let $\mathcal{D}$ be a dataset of smooth 3D-surfaces, partitioned into disjoint classes $\mathit{CL}_j$, $j= 1, \ldots, k$. We show how optimized diffeomorphic registration applied to large numbers of pairs $S,S' \in \mathcal{D}$ can provide descriptive feature vectors to implement automatic classification on $\mathcal{D}$, and generate classifiers invariant by rigid motions in $\mathbb{R}^3$. To enhance accuracy of automatic classification, we enrich the smallest classes $\mathit{CL}_j$ by diffeomorphic interpolation of smooth surfaces between pairs $S,S' \in \mathit{CL}_j$. We also implement small random perturbations of surfaces $S\in \mathit{CL}_j$ by random flows of smooth diffeomorphisms $F_t:\mathbb{R}^3 \to \mathbb{R}^3$. Finally, we test our automatic classification methods on a cardiology data base of discretized mitral valve surfaces.

Ji Shi, Nicolas Charon, Andreas Mang et al.

We introduce a novel, efficient framework for clustering data on high-dimensional, non-Euclidean manifolds that overcomes the computational challenges associated with standard intrinsic methods. The key innovation is the use of the $p$-Fréchet map $F^p : \mathcal{M} \to \mathbb{R}^\ell$ -- defined on a generic metric space $\mathcal{M}$ -- which embeds the manifold data into a lower-dimensional Euclidean space $\mathbb{R}^\ell$ using a set of reference points $\{r_i\}_{i=1}^\ell$, $r_i \in \mathcal{M}$. Once embedded, we can efficiently and accurately apply standard Euclidean clustering techniques such as k-means. We rigorously analyze the mathematical properties of $F^p$ in the Euclidean space and the challenging manifold of $n \times n$ symmetric positive definite matrices $\mathit{SPD}(n)$. Extensive numerical experiments using synthetic and real $\mathit{SPD}(n)$ data demonstrate significant performance gains: our method reduces runtime by up to two orders of magnitude compared to intrinsic manifold-based approaches, all while maintaining high clustering accuracy, including scenarios where existing alternative methods struggle or fail.

Zicong Zhou, Baihan Zhao, Andreas Mang et al.

This paper introduces VPreg, a novel diffeomorphic image registration method. This work provides several improvements to our past work on mesh generation and diffeomorphic image registration. VPreg aims to achieve excellent registration accuracy while controlling the quality of the registration transformations. It ensures a positive Jacobian determinant of the spatial transformation and provides an accurate approximation of the inverse of the registration, a crucial property for many neuroimaging workflows. Unlike conventional methods, VPreg generates this inverse transformation within the group of diffeomorphisms rather than operating on the image space. The core of VPreg is a grid generation approach, referred to as \emph{Variational Principle} (VP), which constructs non-folding grids with prescribed Jacobian determinant and curl. These VP-generated grids guarantee diffeomorphic spatial transformations essential for computational anatomy and morphometry, and provide a more accurate inverse than existing methods. To assess the potential of the proposed approach, we conduct a performance analysis for 150 registrations of brain scans from the OASIS-1 dataset. Performance evaluation based on Dice scores for 35 regions of interest, along with an empirical analysis of the properties of the computed spatial transformations, demonstrates that VPreg outperforms state-of-the-art methods in terms of Dice scores, regularity properties of the computed transformation, and accuracy and consistency of the provided inverse map. We compare our results to ANTs-SyN, Freesurfer-Easyreg, and FSL-Fnirt.

Xiaoyu Wang, Alexandra Valavanis, Azhir Mahmood et al.

The training of deep neural networks predominantly relies on a combination of gradient-based optimisation and back-propagation for the computation of the gradient. While incredibly successful, this approach faces challenges such as vanishing or exploding gradients, difficulties with non-smooth activations, and an inherently sequential structure that limits parallelisation. Lifted training methods offer an alternative by reformulating the nested optimisation problem into a higher-dimensional, constrained optimisation problem where the constraints are no longer enforced directly but penalised with penalty terms. This chapter introduces a unified framework that encapsulates various lifted training strategies, including the Method of Auxiliary Coordinates, Fenchel Lifted Networks, and Lifted Bregman Training, and demonstrates how diverse architectures, such as Multi-Layer Perceptrons, Residual Neural Networks, and Proximal Neural Networks fit within this structure. By leveraging tools from convex optimisation, particularly Bregman distances, the framework facilitates distributed optimisation, accommodates non-differentiable proximal activations, and can improve the conditioning of the training landscape. We discuss the implementation of these methods using block-coordinate descent strategies, including deterministic implementations enhanced by accelerated and adaptive optimisation techniques, as well as implicit stochastic gradient methods. Furthermore, we explore the application of this framework to inverse problems, detailing methodologies for both the training of specialised networks (e.g., unrolled architectures) and the stable inversion of pre-trained networks. Numerical results on standard imaging tasks validate the effectiveness and stability of the lifted Bregman approach compared to conventional training, particularly for architectures employing proximal activations.

Sorena Sarmadi, James J. Winkle, Razan N. Alnahhas et al.

Our work targets automated analysis to quantify the growth dynamics of a population of bacilliform bacteria. We propose an innovative approach to frame-sequence tracking of deformable-cell motion by the automated minimization of a new, specific cost functional. This minimization is implemented by dedicated Boltzmann machines (stochastic recurrent neural networks). Automated detection of cell divisions is handled similarly by successive minimizations of two cost functions, alternating the identification of children pairs and parent identification. We validate the proposed automatic cell tracking algorithm using (i) recordings of simulated cell colonies that closely mimic the growth dynamics of E. coli in microfluidic traps and (ii) real data. On a batch of 1100 simulated image frames, cell registration accuracies per frame ranged from 94.5% to 100%, with a high average. Our initial tests using experimental image sequences (i.e., real data) of E. coli colonies also yield convincing results, with a registration accuracy ranging from 90% to 100%.

Andreas Mang, Amir Gholami, George Biros

We present a parallel distributed-memory algorithm for large deformation diffeomorphic registration of volumetric images that produces large isochoric deformations (locally volume preserving). Image registration is a key technology in medical image analysis. Our algorithm uses a partial differential equation constrained optimal control formulation. Finding the optimal deformation map requires the solution of a highly nonlinear problem that involves pseudo-differential operators, biharmonic operators, and pure advection operators both forward and back- ward in time. A key issue is the time to solution, which poses the demand for efficient optimization methods as well as an effective utilization of high performance computing resources. To address this problem we use a preconditioned, inexact, Gauss-Newton- Krylov solver. Our algorithm integrates several components: a spectral discretization in space, a semi-Lagrangian formulation in time, analytic adjoints, different regularization functionals (including volume-preserving ones), a spectral preconditioner, a highly optimized distributed Fast Fourier Transform, and a cubic interpolation scheme for the semi-Lagrangian time-stepping. We demonstrate the scalability of our algorithm on images with resolution of up to $1024^3$ on the "Maverick" and "Stampede" systems at the Texas Advanced Computing Center (TACC). The critical problem in the medical imaging application domain is strong scaling, that is, solving registration problems of a moderate size of $256^3$---a typical resolution for medical images. We are able to solve the registration problem for images of this size in less than five seconds on 64 x86 nodes of TACC's "Maverick" system.